476 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
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
Hypervelocity Star Candidates in the SEGUE G & K Dwarf Sample
We present 20 candidate hypervelocity stars from the Sloan Extension for
Galactic Understanding and Exploration (SEGUE) G and K dwarf samples. Previous
searches for hypervelocity stars have only focused on large radial velocities;
in this study we also use proper motions to select the candidates. We determine
the hypervelocity likelihood of each candidate by means of Monte Carlo
simulations, considering the significant errors often associated with high
proper motion stars. We find that nearly half of the candidates exceed their
escape velocities with at least 98% probability. Every candidate also has less
than a 25% chance of being a high-velocity fluke within the SEGUE sample. Based
on orbits calculated using the observed six-dimensional positions and
velocities, few, if any, of these candidates originate from the Galactic
center. If these candidates are truly hypervelocity stars, they were not
ejected by interactions with the Milky Way's supermassive black hole. This
calls for a more serious examination of alternative hypervelocity-star ejection
scenarios.Comment: 8 pages, 5 figures, published in ApJ, this version includes all
figures as intende
DNA unzipped under a constant force exhibits multiple metastable intermediates
Single molecule studies, at constant force, of the separation of
double-stranded DNA into two separated single strands may provide information
relevant to the dynamics of DNA replication. At constant applied force, theory
predicts that the unzipped length as a function of time is characterized by
jumps during which the strands separate rapidly, followed by long pauses where
the number of separated base pairs remains constant. Here, we report previously
uncharacterized observations of this striking behavior carried out on a number
of identical single molecules simultaneously. When several single lphage
molecules are subject to the same applied force, the pause positions are
reproducible in each. This reproducibility shows that the positions and
durations of the pauses in unzipping provide a sequence-dependent molecular
fingerprint. For small forces, the DNA remains in a partially unzipped state
for at least several hours. For larger forces, the separation is still
characterized by jumps and pauses, but the double-stranded DNA will completely
unzip in less than 30 min
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
On the equilibrium morphology of systems drawn from spherical collapse experiments
We present a purely theoretical study of the morphological evolution of
self-gravitating systems formed through the dissipationless collapse of N-point
sources. We explore the effects of resolution in mass and length on the growth
of triaxial structures formed by an instability triggered by an excess of
radial orbits. We point out that as resolution increases, the equilibria shift,
from mildly prolate, to oblate. A number of particles N ~= 100000 or larger is
required for convergence of axial aspect ratios. An upper bound for the
softening, e ~ 1/256, is also identified. We then study the properties of a set
of equilibria formed from scale-free cold initial mass distributions, ro ~ r^-g
with 0 <= g <= 2. Oblateness is enhanced for initially more peaked structures
(larger values of g). We map the run of density in space and find no evidence
for a power-law inner structure when g <= 3/2 down to a mass fraction <~0.1 per
cent of the total. However, when 3/2 < g <= 2, the mass profile in equilibrium
is well matched by a power law of index ~g out to a mass fraction ~ 10 per
cent. We interpret this in terms of less-effective violent relaxation for more
peaked profiles when more phase mixing takes place at the centre. We map out
the velocity field of the equilibria and note that at small radii the velocity
coarse-grained distribution function (DF) is Maxwellian to a very good
approximation.Comment: 16 page
The Candidate Intermediate-Mass Black Hole in the Globular Cluster M54
Ibata et al. reported evidence for density and kinematic cusps in the
Galactic globular cluster M54, possibly due to the presence of a 9400
solar-mass black hole. Radiative signatures of accretion onto M54's candidate
intermediate-mass black hole (IMBH) could bolster the case for its existence.
Analysis of new Chandra and recent Hubble Space Telescope astrometry rules out
the X-ray counterpart to the candidate IMBH suggested by Ibata et al. If an
IMBH exists in M54, then it has an Eddington ratio of L(0.3-8 keV) / L(Edd) <
1.4 x 10^(-10), more similar to that of the candidate IMBH in M15 than that in
G1. From new imaging with the NRAO Very Large Array, the luminosity of the
candidate IMBH is L(8.5 GHz) < 3.6 x 10^29 ergs/s (3 sigma). Two background
active galaxies discovered toward M54 could serve as probes of its intracluster
medium.Comment: 4 pages; 2 figures; emulateapj.cls; to appear in A
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