4,100 research outputs found
Slow nucleic acid unzipping kinetics from sequence-defined barriers
Recent experiments on unzipping of RNA helix-loop structures by force have
shown that about 40-base molecules can undergo kinetic transitions between two
well-defined `open' and `closed' states, on a timescale = 1 sec [Liphardt et
al., Science 297, 733-737 (2001)]. Using a simple dynamical model, we show that
these phenomena result from the slow kinetics of crossing large free energy
barriers which separate the open and closed conformations. The dependence of
barriers on sequence along the helix, and on the size of the loop(s) is
analyzed. Some DNAs and RNAs sequences that could show dynamics on different
time scales, or three(or more)-state unzipping, are proposed.Comment: 8 pages Revtex, including 4 figure
Elasticity model of a supercoiled DNA molecule
Within a simple elastic theory, we study the elongation versus force
characteristics of a supercoiled DNA molecule at thermal equilibrium in the
regime of small supercoiling. The partition function is mapped to the path
integral representation for a quantum charged particle in the field of a
magnetic monopole with unquantized charge.
We show that the theory is singular in the continuum limit and must be
regularised at an intermediate length scale. We find good agreement with
existing experimental data, and point out how to measure the twist rigidity
accurately.Comment: Latex, 4 pages. The figure contains new experimental data, giving a
new determination of the twist rigidit
Continuum model for polymers with finite thickness
We consider the continuum limit of a recently-introduced model for
discretized thick polymers, or tubes. We address both analytically and
numerically how the polymer thickness influences the decay of tangent-tangent
correlations and find how the persistence length scales with the thickness and
the torsional rigidity of the tube centerline. At variance with the worm-like
chain model, the phase diagram that we obtain for a continuous tube is richer;
in particular, for a given polymer thickness there exists a threshold value for
the centerline torsional rigidity separating a simple exponential decay of the
tangent-tangent correlation from an oscillatory one.Comment: 8 pages, 4 figures. Accepted for publication in J. Phys.
In-flight dissipation as a mechanism to suppress Fermi acceleration
Some dynamical properties of time-dependent driven elliptical-shaped billiard
are studied. It was shown that for the conservative time-dependent dynamics the
model exhibits the Fermi acceleration [Phys. Rev. Lett. 100, 014103 (2008)]. On
the other hand, it was observed that damping coefficients upon collisions
suppress such phenomenon [Phys. Rev. Lett. 104, 224101 (2010)]. Here, we
consider a dissipative model under the presence of in-flight dissipation due to
a drag force which is assumed to be proportional to the square of the
particle's velocity. Our results reinforce that dissipation leads to a phase
transition from unlimited to limited energy growth. The behaviour of the
average velocity is described using scaling arguments.Comment: 4 pages, 5 figure
Rotator and extender ferroelectrics: Importance of the shear coefficient to the piezoelectric properties of domain-engineered crystals and ceramics
The importance of a high shear coefficient d15 (or d24) to the piezoelectric
properties of domain-engineered and polycrystalline ferroelectrics is
discussed. The extent of polarization rotation, as a mechanism of piezoelectric
response, is directly correlated to the shear coefficient. The terms "rotator"
and "extender" are introduced to distinguish the contrasting behaviors of
crystals such as 4mm BaTiO3 and PbTiO3. In "rotator" ferroelectrics, where d15
is high relative to the longitudinal coefficient d33, polarization rotation is
the dominant mechanism of piezoelectric response; the maximum longitudinal
piezoelectric response is found away from the polar axis. In "extender"
ferroelectrics, d15 is low and the collinear effect dominates; the maximum
piezoelectric response is found along the polar axis. A variety of 3m, mm2 and
4mm ferroelectrics, with various crystal structures based on oxygen octahedra,
are classified in this way. It is shown that the largest piezoelectric
anisotropies d15/d33 are always found in 3m crystals; this is a result of the
intrinsic electrostrictive anisotropy of the constituent oxygen octahedra.
Finally, for a given symmetry, the piezoelectric anisotropy increases close to
ferroelectric-ferroelectric phase transitions; this includes morphotropic phase
boundaries and temperature induced polymorphic transitions.Comment: accepted in J. Appl. Phy
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
Hamiltonians for curves
We examine the equilibrium conditions of a curve in space when a local energy
penalty is associated with its extrinsic geometrical state characterized by its
curvature and torsion. To do this we tailor the theory of deformations to the
Frenet-Serret frame of the curve. The Euler-Lagrange equations describing
equilibrium are obtained; Noether's theorem is exploited to identify the
constants of integration of these equations as the Casimirs of the euclidean
group in three dimensions. While this system appears not to be integrable in
general, it {\it is} in various limits of interest. Let the energy density be
given as some function of the curvature and torsion, . If
is a linear function of either of its arguments but otherwise arbitrary, we
claim that the first integral associated with rotational invariance permits the
torsion to be expressed as the solution of an algebraic equation in
terms of the bending curvature, . The first integral associated with
translational invariance can then be cast as a quadrature for or for
.Comment: 17 page
Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers
that condense into a compact structure. We use optical tweezers to pull
condensed fibers and investigate the decondensation transition by measuring
force-extension curves (FECs). A characteristic plateau force (around 10 pN)
and hysteresis between the pulling and relaxation cycles are observed for
different dendrimer sizes, indicating the existence of a first-order transition
between two phases (condensed and extended) of the fiber. The fact that we can
reproduce the same FECs in the absence of additional dendrimers in the buffer
medium indicates that dendrimers remain irreversibly bound to the DNA backbone.
Upon salt variation FECs change noticeably confirming that electrostatic forces
drive the condensation transition. Finally, we propose a simple model for the
decondensing transition that qualitatively reproduces the FECs and which is
confirmed by AFM images.Comment: Latex version, 4 pages+3 color figure
Topological interactions in systems of mutually interlinked polymer rings
The topological interaction arising in interlinked polymeric rings such as
DNA catenanes is considered. More specifically, the free energy for a pair of
linked random walk rings is derived where the distance between two segments
each of which is part of a different ring is kept constant. The topology
conservation is imposed by the Gauss invariant. A previous approach (M.Otto,
T.A. Vilgis, Phys.Rev.Lett. {\bf 80}, 881 (1998)) to the problem is refined in
several ways. It is confirmed, that asymptotically, i.e. for large
where is average size of single random walk ring, the effective
topological interaction (free energy) scales .Comment: 16 pages, 3 figur
A length-dynamic Tonks gas theory of histone isotherms
We find exact solutions to a new one-dimensional (1D) interacting particle
theory and apply the results to the adsorption and wrapping of polymers (such
as DNA) around protein particles (such as histones). Each adsorbed protein is
represented by a Tonks gas particle. The length of each particle is a degree of
freedom that represents the degree of DNA wrapping around each histone.
Thermodynamic quantities are computed as functions of wrapping energy, adsorbed
histone density, and bulk histone concentration (or chemical potential); their
experimental signatures are also discussed. Histone density is found to undergo
a two-stage adsorption process as a function of chemical potential, while the
mean coverage by high affinity proteins exhibits a maximum as a function of the
chemical potential. However, {\it fluctuations} in the coverage are
concurrently maximal. Histone-histone correlation functions are also computed
and exhibit rich two length scale behavior.Comment: 5 pp, 3 fig
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