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