521 research outputs found
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
Pause Point Spectra in DNA Constant-Force Unzipping
Under constant applied force, the separation of double-stranded DNA into two
single strands is known to proceed through a series of pauses and jumps. Given
experimental traces of constant-force unzipping, we present a method whereby
the locations of pause points can be extracted in the form of a pause point
spectrum. A simple theoretical model of DNA constant-force unzipping is
demonstrated to produce good agreement with the experimental pause point
spectrum of lambda phage DNA. The locations of peaks in the experimental and
theoretical pause point spectra are found to be nearly coincident below 6000
bp. The model only requires the sequence, temperature and a set of empirical
base pair binding and stacking energy parameters, and the good agreement with
experiment suggests that pause points are primarily determined by the DNA
sequence. The model is also used to predict pause point spectra for the
BacterioPhage PhiX174 genome. The algorithm for extracting the pause point
spectrum might also be useful for studying related systems which exhibit
pausing behavior such as molecular motors.Comment: 15 pages, 12 figure
Probing the mechanical unzipping of DNA
A study of the micromechanical unzipping of DNA in the framework of the
Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique
that allows accurate determination of the dependence of the unzipping forces on
unzipping speed and temperature. Our findings agree quantitatively with
experimental results for homogeneous DNA, and for -phage DNA we
reproduce the recently obtained experimental force-temperature phase diagram.
Finally, we argue that there may be fundamental differences between {\em in
vivo} and {\em in vitro} DNA unzipping
Inferring DNA sequences from mechanical unzipping: an ideal-case study
We introduce and test a method to predict the sequence of DNA molecules from
in silico unzipping experiments. The method is based on Bayesian inference and
on the Viterbi decoding algorithm. The probability of misprediction decreases
exponentially with the number of unzippings, with a decay rate depending on the
applied force and the sequence content.Comment: Source as TeX file with ps figure
Bar-Halo Friction in Galaxies II: Metastability
It is well-established that strong bars rotating in dense halos generally
slow down as they lose angular momentum to the halo through dynamical friction.
Angular momentum exchanges between the bar and halo particles take place at
resonances. While some particles gain and others lose, friction arises when
there is an excess of gainers over losers. This imbalance results from the
generally decreasing numbers of particles with increasing angular momentum, and
friction can therefore be avoided if there is no gradient in the density of
particles across the major resonances. Here we show that anomalously weak
friction can occur for this reason if the pattern speed of the bar fluctuates
upwards. After such an event, the density of resonant halo particles has a
local inflexion created by the earlier exchanges, and bar slowdown can be
delayed for a long period; we describe this as a metastable state. We show that
this behavior in purely collisionless N-body simulations is far more likely to
occur in methods with adaptive resolution. We also show that the phenomenon
could arise in nature, since bar-driven gas inflow could easily raise the bar
pattern speed enough to reach the metastable state. Finally, we demonstrate
that mild external, or internal, perturbations quickly restore the usual
frictional drag, and it is unlikely therefore that a strong bar in a galaxy
having a dense halo could rotate for a long period without friction.Comment: 13 pages, 11 figures, to appear in Ap
Non-equilibrium transport through a vertical quantum dot in the absence of spin-flip energy relaxation
We investigate non-equilibrium transport in the absence of spin-flip energy
relaxation in a few-electron quantum dot artificial atom. Novel non-equilibrium
tunneling processes involving high-spin states which cannot be excited from the
ground state because of spin-blockade, and other processes involving more than
two charge states are observed. These processes cannot be explained by orthodox
Coulomb blockade theory. The absence of effective spin relaxation induces
considerable fluctuation of the spin, charge, and total energy of the quantum
dot. Although these features are revealed clearly by pulse excitation
measurements, they are also observed in conventional dc current characteristics
of quantum dots.Comment: accepted for publication in Phys. Rev.Let
Transient current spectroscopy of a quantum dot in the Coulomb blockade regime
Transient current spectroscopy is proposed and demonstrated in order to
investigate the energy relaxation inside a quantum dot in the Coulomb blockade
regime. We employ a fast pulse signal to excite an AlGaAs/GaAs quantum dot to
an excited state, and analyze the non-equilibrium transient current as a
function of the pulse length. The amplitude and time-constant of the transient
current are sensitive to the ground and excited spin states. We find that the
spin relaxation time is longer than, at least, a few microsecond.Comment: 5 pages, 3 figure
Unzipping Kinetics of Double-Stranded DNA in a Nanopore
We studied the unzipping kinetics of single molecules of double-stranded DNA
by pulling one of their two strands through a narrow protein pore. PCR analysis
yielded the first direct proof of DNA unzipping in such a system. The time to
unzip each molecule was inferred from the ionic current signature of DNA
traversal. The distribution of times to unzip under various experimental
conditions fit a simple kinetic model. Using this model, we estimated the
enthalpy barriers to unzipping and the effective charge of a nucleotide in the
pore, which was considerably smaller than previously assumed.Comment: 10 pages, 5 figures, Accepted: Physics Review Letter
Carrier relaxation in GaAs v-groove quantum wires and the effects of localization
Carrier relaxation processes have been investigated in GaAs/AlGaAs v-groove
quantum wires (QWRs) with a large subband separation (46 meV). Signatures of
inhibited carrier relaxation mechanisms are seen in temperature-dependent
photoluminescence (PL) and photoluminescence-excitation (PLE) measurements; we
observe strong emission from the first excited state of the QWR below ~50 K.
This is attributed to reduced inter-subband relaxation via phonon scattering
between localized states. Theoretical calculations and experimental results
indicate that the pinch-off regions, which provide additional two-dimensional
confinement for the QWR structure, have a blocking effect on relaxation
mechanisms for certain structures within the v-groove. Time-resolved PL
measurements show that efficient carrier relaxation from excited QWR states
into the ground state, occurs only at temperatures > 30 K. Values for the low
temperature radiative lifetimes of the ground- and first excited-state excitons
have been obtained (340 ps and 160 ps respectively), and their corresponding
localization lengths along the wire estimated.Comment: 9 pages, 8 figures, submitted to Phys. Rev. B Attempted to correct
corrupt figure
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