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

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

The H I Environment Of The M101 Group

We present a wide (8. Degree-Sign 5 Multiplication-Sign 6. Degree-Sign 7, 1050 Multiplication-Sign 825 kpc), deep ({sigma}{sub N{sub H{sub {sub {sub i}}}}}10{sup 16.8}-10{sup 17.5} cm{sup -2}) neutral hydrogen (H I) map of the M101 galaxy group. We identify two new H I sources in the group environment, one an extremely low surface brightness (and hitherto unknown) dwarf galaxy, and the other a starless H I cloud, possibly primordial in origin. Our data show that M101\u27s extended H I envelope takes the form of a {approx}100 kpc long tidal loop or plume of H I extending to the southwest of the galaxy. The plume has an H I mass of {approx}10{sup 8} M{sub Sun} and a peak column density of N{sub H{sub i}}= 5 Multiplication-Sign 10{sup 17} cm{sup -2}, and while it rotates with the main body of M101, it shows kinematic peculiarities suggestive of a warp or flaring out of the rotation plane of the galaxy. We also find two new H I clouds near the plume with masses {approx}10{sup 7} M{sub Sun }, similar to H I clouds seen in the M81/M82 group, and likely also tidal in nature. Comparing to deep optical imaging of the M101 group, neithermore » the plume nor the clouds have any extended optical counterparts down to a limiting surface brightness of {mu}{sub B} = 29.5. We also trace H I at intermediate velocities between M101 and NGC 5474, strengthening the case for a recent interaction between the two galaxies. The kinematically complex H I structure in the M101 group, coupled with the optical morphology of M101 and its companions, suggests that the group is in a dynamically active state that is likely common for galaxies in group environments.« les

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