66 research outputs found
Blinking statistics of a molecular beacon triggered by end-denaturation of DNA
We use a master equation approach based on the Poland-Scheraga free energy
for DNA denaturation to investigate the (un)zipping dynamics of a denaturation
wedge in a stretch of DNA, that is clamped at one end. In particular, we
quantify the blinking dynamics of a fluorophore-quencher pair mounted within
the denaturation wedge. We also study the behavioural changes in the presence
of proteins, that selectively bind to single-stranded DNA. We show that such a
setup could be well-suited as an easy-to-implement nanodevice for sensing
environmental conditions in small volumes.Comment: 14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat
special issue on diffusio
A model for melting of confined DNA
When DNA molecules are heated they denature. This occurs locally so that
loops of molten single DNA strands form, connected by intact double-stranded
DNA pieces. The properties of this "melting" transition have been intensively
investigated. Recently there has been a surge of interest in this question,
caused by experiments determining the properties of partially bound DNA
confined to nanochannels. But how does such confinement affect the melting
transition? To answer this question we introduce, and solve a model predicting
how confinement affects the melting transition for a simple model system by
first disregarding the effect of self-avoidance. We find that the transition is
smoother for narrower channels. By means of Monte-Carlo simulations we then
show that a model incorporating self-avoidance shows qualitatively the same
behaviour and that the effect of confinement is stronger than in the ideal
case.Comment: 5 pages, 4 figures, supplementary materia
Electromagnetic response of a dipole-coupled ellipsoidal bilayer
©2006 The American Physical Society. This paper was selected for the April 1, 2004 issue of Virtual Journal of Biological Physics Research, available at http://www.vjbio.org .We derive an expression for the polarizability of an ellipsoidally shaped cell-like structure at field frequencies where membrane molecular resonances ~vibrational and electronic! are important. We first present analytical results for the dielectric function of a flat, dipole coupled, bilayer consisting of molecules with one prominent resonance frequency. Due to the nature of the dipole coupling the dielectric function is different for the field being parallel or perpendicular to the bilayer normal with two new resonance frequencies v5v ˜ 0i and v5v ˜ 0' . We then combine this anisotropic bilayer dielectric function with the analytical solution of Gauss equation for an ellipsoid with an anisotropic coating ~the coating dielectric function being different parallel and perpendicular to the coating normal! in order to find the polarizability of an ellipsoidal bilayer membrane. In
particular, we find that for a thin-walled ~compared to the size of the cell! membrane the resonance frequencies of the polarizability are the same as for a flat bilayer ~independent of the cell shape!. However, our analytic result for the geometric weights for the oscillator strengths is sensitive to the shape; the geometric weight for the v5v ˜ 0' (v5v ˜ 0i) peak is largest when the external field is along the largest ~smallest! axis. The geometric weights are shown to be constrained by three sum rules
Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins
We investigate the translocation of a stiff polymer consisting of M monomers
through a nanopore in a membrane, in the presence of binding particles
(chaperones) that bind onto the polymer, and partially prevent backsliding of
the polymer through the pore. The process is characterized by the rates: k for
the polymer to make a diffusive jump through the pore, q for unbinding of a
chaperone, and the rate q kappa for binding (with a binding strength kappa);
except for the case of no binding kappa=0 the presence of the chaperones give
rise to an effective force that drives the translocation process. Based on a
(2+1) variate master equation, we study in detail the coupled dynamics of
diffusive translocation and (partial) rectification by the binding proteins. In
particular, we calculate the mean translocation time as a function of the
various physical parameters.Comment: 22 pages, 5 figures, IOP styl
Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials
We investigate the coalescence of two DNA-bubbles initially located at weak
segments and separated by a more stable barrier region in a designed construct
of double-stranded DNA. The characteristic time for bubble coalescence and the
corresponding distribution are derived, as well as the distribution of
coalescence positions along the barrier. Below the melting temperature, we find
a Kramers-type barrier crossing behaviour, while at high temperatures, the
bubble corners perform drift-diffusion towards coalescence. The results are
obtained by mapping the bubble dynamics on the problem of two vicious walkers
in opposite potentials.Comment: 7 pages, 4 figure
Fluctuations in Polymer Translocation
We investigate a model of chaperone-assisted polymer translocation through a
nanopore in a membrane. Translocation is driven by irreversible random
sequential absorption of chaperone proteins that bind to the polymer on one
side of the membrane. The proteins are larger than the pore and hence the
backward motion of the polymer is inhibited. This mechanism rectifies Brownian
fluctuations and results in an effective force that drags the polymer in a
preferred direction. The translocated polymer undergoes an effective biased
random walk and we compute the corresponding diffusion constant. Our methods
allow us to determine the large deviation function which, in addition to
velocity and diffusion constant, contains the entire statistics of the
translocated length.Comment: 20 pages, 6 figure
Fluctuations of a driven membrane in an electrolyte
We develop a model for a driven cell- or artificial membrane in an
electrolyte. The system is kept far from equilibrium by the application of a DC
electric field or by concentration gradients, which causes ions to flow through
specific ion-conducting units (representing pumps, channels or natural pores).
We consider the case of planar geometry and Debye-H\"{u}ckel regime, and obtain
the membrane equation of motion within Stokes hydrodynamics. At steady state,
the applied field causes an accumulation of charges close to the membrane,
which, similarly to the equilibrium case, can be described with renormalized
membrane tension and bending modulus. However, as opposed to the equilibrium
situation, we find new terms in the membrane equation of motion, which arise
specifically in the out-of-equilibrium case. We show that these terms lead in
certain conditions to instabilities.Comment: 7 pages, 2 figures. submitted to Europhys. Let
Exact steady-state velocity of ratchets driven by random sequential adsorption
We solve the problem of discrete translocation of a polymer through a pore,
driven by the irreversible, random sequential adsorption of particles on one
side of the pore. Although the kinetics of the wall motion and the deposition
are coupled, we find the exact steady-state distribution for the gap between
the wall and the nearest deposited particle. This result enables us to
construct the mean translocation velocity demonstrating that translocation is
faster when the adsorbing particles are smaller. Monte-Carlo simulations also
show that smaller particles gives less dispersion in the ratcheted motion. We
also define and compare the relative efficiencies of ratcheting by deposition
of particles with different sizes and we describe an associated
"zone-refinement" process.Comment: 11 pages, 4 figures New asymptotic result for low chaperone density
added. Exact translocation velocity is proportional to (chaperone
density)^(1/3
Extension of nano-confined DNA: quantitative comparison between experiment and theory
The extension of DNA confined to nanochannels has been studied intensively
and in detail. Yet quantitative comparisons between experiments and model
calculations are difficult because most theoretical predictions involve
undetermined prefactors, and because the model parameters (contour length, Kuhn
length, effective width) are difficult to compute reliably, leading to
substantial uncertainties. Here we use a recent asymptotically exact theory for
the DNA extension in the "extended de Gennes regime" that allows us to compare
experimental results with theory. For this purpose we performed new
experiments, measuring the mean DNA extension and its standard deviation while
varying the channel geometry, dye intercalation ratio, and ionic buffer
strength. The experimental results agree very well with theory at high ionic
strengths, indicating that the model parameters are reliable. At low ionic
strengths the agreement is less good. We discuss possible reasons. Our approach
allows, in principle, to measure the Kuhn length and effective width of a
single DNA molecule and more generally of semiflexible polymers in solution.Comment: Revised version, 6 pages, 2 figures, 1 table, supplementary materia
The prolate-to-oblate shape transition of phospholipid vesicles in response to frequency variation of an AC electric field can be explained by the dielectric anisotropy of a phospholipid bilayer
The external electric field deforms flaccid phospholipid vesicles into
spheroidal bodies, with the rotational axis aligned with its direction.
Deformation is frequency dependent: in the low frequency range (~ 1 kHz), the
deformation is typically prolate, while increasing the frequency to the 10 kHz
range changes the deformation to oblate. We attempt to explain this behaviour
with a theoretical model, based on the minimization of the total free energy of
the vesicle. The energy terms taken into account include the membrane bending
energy and the energy of the electric field. The latter is calculated from the
electric field via the Maxwell stress tensor, where the membrane is modelled as
anisotropic lossy dielectric. Vesicle deformation in response to varying
frequency is calculated numerically. Using a series expansion, we also derive a
simplified expression for the deformation, which retains the frequency
dependence of the exact expression and may provide a better substitute for the
series expansion used by Winterhalter and Helfrich, which was found to be valid
only in the limit of low frequencies. The model with the anisotropic membrane
permittivity imposes two constraints on the values of material constants:
tangential component of dielectric permittivity tensor of the phospholipid
membrane must exceed its radial component by approximately a factor of 3; and
the membrane conductivity has to be relatively high, approximately one tenth of
the conductivity of the external aqueous medium.Comment: 17 pages, 6 figures; accepted for publication in J. Phys.: Condens.
Matte
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