Stretching and relaxation dynamics in double stranded DNA

We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special attention to the opening-closing dynamics of double-stranded DNA molecules which are forced into non-equilibrium conformations. Mechanical stress imposed at one terminal end of the DNA molecule brings it into a partially opened configuration. We examine the subsequent relaxation dynamics connected with energy exchange processes between the various degrees of freedom and structural rearrangements leading to complete recombination to the double-stranded conformation. The similarities and differences between the relaxation dynamics for a planar ladder-like DNA molecule and a twisted one are discussed in detail. In this way we show that the attainment of a quasi-equilibrium regime proceeds faster in the case of the twisted DNA form than for its thus less flexible ladder counterpart. Furthermore we find that the velocity of the complete recombination of the DNA molecule is lower than the velocity imposed by the forcing unit which is in compliance with the experimental observations for the opening-closing cycle of DNA molecules.Comment: 21 pages, 9 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 $\lambda$-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

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

Radiative Lifetimes of Single Excitons in Semiconductor Quantum Dots- Manifestation of the Spatial Coherence Effect

Using time correlated single photon counting combined with temperature dependent diffraction limited confocal photoluminescence spectroscopy we accurately determine, for the first time, the intrinsic radiative lifetime of single excitons confined within semiconductor quantum dots. Their lifetime is one (two) orders of magnitude longer than the intrinsic radiative lifetime of single excitons confined in semiconductor quantum wires (wells) of comparable confining dimensions. We quantitatively explain this long radiative time in terms of the reduced spatial coherence between the confined exciton dipole moment and the radiation electromagnetic field.Comment: 4 pages, 3 figure

The Evolution of Cuspy Triaxial Galaxies Harboring Central Black Holes

We use numerical simulations to study the evolution of triaxial elliptical galaxies with central black holes. In contrast to earlier numerical studies which used galaxy models with central density ``cores,'' our galaxies have steep central cusps, like those observed in real ellipticals. As a black hole grows in these cuspy triaxial galaxies, the inner regions become rounder owing to chaos induced in the orbit families which populate the model. At larger radii, however, the models maintain their triaxiality, and orbital analyses show that centrophilic orbits there resist stochasticity over many dynamical times. While black hole induced evolution is strong in the inner regions of these galaxies, and reaches out beyond the nominal ``sphere of influence'' of a black hole, our simulations do not show evidence for a rapid {\it global} transformation of the host. The triaxiality of observed elliptical galaxies is therefore not inconsistent with the presence of supermassive black holes at their centers.Comment: 15 pages, 7 figures (1 color). Accepted for publication in Ap

The stellar disk thickness of LSB galaxies

We present surface photometry results for a sample of eleven edge-on galaxies observed with the 6m telescope at the Special Astrophysical Observatory (Russia). The photometric scale length, scale height, and central surface brightness of the stellar disks of our sample galaxies are estimated. We show that four galaxies in our sample, which are visually referred as objects of the lowest surface brightness class in the Revised Flat Galaxies Catalog, have bona fide low surface brightness (LSB) disks. We find from the comparison of photometric scales that the stellar disks of LSB galaxies are thinner than those of high surface brightness (HSB) ones. There is a clear correlation between the central surface brightness of the stellar disk and its vertical to radial scale ratio. The masses of spherical subsystems (dark halo + bulge) and the dark halo masses are obtained for the sample galaxies based on the thickness of their stellar disks. The LSB galaxies tend to harbor more massive spherical subsystems than the HSB objects, whereas no systematic difference in the dark halo masses between LSB and HSB galaxies is found. At the same time, the inferred mass-to-luminosity ratio for the LSB disks appears to be systematically higher than for HSB disks.Comment: 33 pages with 17 Postscript figures, uses aastex.cls, accepted by Ap

A General Formula for Black Hole Gravitational Wave Kicks

Although the gravitational wave kick velocity in the orbital plane of coalescing black holes has been understood for some time, apparently conflicting formulae have been proposed for the dominant out-of-plane kick, each a good fit to different data sets. This is important to resolve because it is only the out-of-plane kicks that can reach more than 500 km/s and can thus eject merged remnants from galaxies. Using a different ansatz for the out-of-plane kick, we show that we can fit almost all existing data to better than 5 %. This is good enough for any astrophysical calculation, and shows that the previous apparent conflict was only because the two data sets explored different aspects of the kick parameter space.Comment: 14 pages