540 research outputs found
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
A Clinical Trial
Purpose The aim of this study was the systematic image quality evaluation of
coronary CT angiography (CTA), reconstructed with the 3 different levels of
adaptive iterative dose reduction (AIDR 3D) and compared to filtered back
projection (FBP) with quantum denoising software (QDS). Methods Standard-dose
CTA raw data of 30 patients with mean radiation dose of 3.2 ± 2.6 mSv were
reconstructed using AIDR 3D mild, standard, strong and compared to FBP/QDS.
Objective image quality comparison (signal, noise, signal-to-noise ratio
(SNR), contrast-to-noise ratio (CNR), contour sharpness) was performed using
21 measurement points per patient, including measurements in each coronary
artery from proximal to distal. Results Objective image quality parameters
improved with increasing levels of AIDR 3D. Noise was lowest in AIDR 3D strong
(p≤0.001 at 20/21 measurement points; compared with FBP/QDS). Signal and
contour sharpness analysis showed no significant difference between the
reconstruction algorithms for most measurement points. Best coronary SNR and
CNR were achieved with AIDR 3D strong. No loss of SNR or CNR in distal
segments was seen with AIDR 3D as compared to FBP. Conclusions On standard-
dose coronary CTA images, AIDR 3D strong showed higher objective image quality
than FBP/QDS without reducing contour sharpness
Thermal Fluctuations of Elastic Filaments with Spontaneous Curvature and Torsion
We study the effects of thermal flucutations on thin elastic filaments with
spontaneous curvature and torsion. We derive analytical expressions for the
orientational correlation functions and for the persistence length of helices,
and find that this length varies non-monotonically with the strength of thermal
fluctuations. In the weak fluctuation regime, the persistence length of a
spontaneously twisted helix has three resonance peaks as a function of the
twist rate. In the limit of strong fluctuations, all memory of the helical
shape is lost.Comment: 1 figur
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
Force and kinetic barriers in unzipping of DNA
A theory of the unzipping of double-stranded (ds) DNA is presented, and is
compared to recent micromanipulation experiments. It is shown that the
interactions which stabilize the double helix and the elastic rigidity of
single strands (ss) simply determine the sequence dependent =12 pN force
threshold for DNA strand separation. Using a semi-microscopic model of the
binding between nucleotide strands, we show that the greater rigidity of the
strands when formed into dsDNA, relative to that of isolated strands, gives
rise to a potential barrier to unzipping. The effects of this barrier are
derived analytically. The force to keep the extremities of the molecule at a
fixed distance, the kinetic rates for strand unpairing at fixed applied force,
and the rupture force as a function of loading rate are calculated. The
dependence of the kinetics and of the rupture force on molecule length is also
analyzed.Comment: Revtex file + 6 eps Figures; published in Proc. Natl. Acad. Sci. USA
98, 8608 (2001
Unzipping Dynamics of Long DNAs
The two strands of the DNA double helix can be `unzipped' by application of
15 pN force. We analyze the dynamics of unzipping and rezipping, for the case
where the molecule ends are separated and re-approached at constant velocity.
For unzipping of 50 kilobase DNAs at less than about 1000 bases per second,
thermal equilibrium-based theory applies. However, for higher unzipping
velocities, rotational viscous drag creates a buildup of elastic torque to
levels above kBT in the dsDNA region, causing the unzipping force to be well
above or well below the equilibrium unzipping force during respectively
unzipping and rezipping, in accord with recent experimental results of Thomen
et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect
of sequence on unzipping and rezipping, and the transient delay in buildup of
the unzipping force due to the approach to the steady state.Comment: 15 pages Revtex file including 9 figure
Theory of biopolymer stretching at high forces
We provide a unified theory for the high force elasticity of biopolymers
solely in terms of the persistence length, , and the monomer spacing,
. When the force f>\fh \sim k_BT\xi_p/a^2 the biopolymers behave as Freely
Jointed Chains (FJCs) while in the range \fl \sim k_BT/\xi_p < f < \fh the
Worm-like Chain (WLC) is a better model. We show that can be estimated
from the force extension curve (FEC) at the extension
(normalized by the contour length of the biopolymer). After validating the
theory using simulations, we provide a quantitative analysis of the FECs for a
diverse set of biopolymers (dsDNA, ssRNA, ssDNA, polysaccharides, and
unstructured PEVK domain of titin) for . The success of a specific
polymer model (FJC or WLC) to describe the FEC of a given biopolymer is
naturally explained by the theory. Only by probing the response of biopolymers
over a wide range of forces can the -dependent elasticity be fully
described.Comment: 20 pages, 4 figure
Single Molecule Statistics and the Polynucleotide Unzipping Transition
We present an extensive theoretical investigation of the mechanical unzipping
of double-stranded DNA under the influence of an applied force. In the limit of
long polymers, there is a thermodynamic unzipping transition at a critical
force value of order 10 pN, with different critical behavior for homopolymers
and for random heteropolymers. We extend results on the disorder-averaged
behavior of DNA's with random sequences to the more experimentally accessible
problem of unzipping a single DNA molecule. As the applied force approaches the
critical value, the double-stranded DNA unravels in a series of discrete,
sequence-dependent steps that allow it to reach successively deeper energy
minima. Plots of extension versus force thus take the striking form of a series
of plateaus separated by sharp jumps. Similar qualitative features should
reappear in micromanipulation experiments on proteins and on folded RNA
molecules. Despite their unusual form, the extension versus force curves for
single molecules still reveal remnants of the disorder-averaged critical
behavior. Above the transition, the dynamics of the unzipping fork is related
to that of a particle diffusing in a random force field; anomalous,
disorder-dominated behavior is expected until the applied force exceeds the
critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure
Elasticity of semiflexible polymers with and without self-interactions
A {\it new} formula for the force vs extension relation is derived from the
discrete version of the so called {\it worm like chain} model. This formula
correctly fits some recent experimental data on polymer stretching and some
numerical simulations with pairwise repulsive potentials. For a more realistic
Lennard-Jones potential the agreement with simulations is found to be good when
the temperature is above the temperature. For lower temperatures a
plateau emerges, as predicted by some recent experimental and theoretical
results, and our formula gives good results only in the high force regime. We
briefly discuss how other kinds of self-interactions are expected to affect the
elasticity of the polymer.Comment: 8 pages, 10 figure
Tightness of slip-linked polymer chains
We study the interplay between entropy and topological constraints for a
polymer chain in which sliding rings (slip-links) enforce pair contacts between
monomers. These slip-links divide a closed ring polymer into a number of
sub-loops which can exchange length between each other. In the ideal chain
limit, we find the joint probability density function for the sizes of segments
within such a slip-linked polymer chain (paraknot). A particular segment is
tight (small in size) or loose (of the order of the overall size of the
paraknot) depending on both the number of slip-links it incorporates and its
competition with other segments. When self-avoiding interactions are included,
scaling arguments can be used to predict the statistics of segment sizes for
certain paraknot configurations.Comment: 10 pages, 6 figures, REVTeX
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