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

Electrokinetic optimization of a micromixer for lab-on-chip applications

This paper is concerned with the optimization of an electrokinetic micromixer suitable for Lab-on-Chip and other microfluidic applications. The mixing concept is based on the combination of an alternating electrical excitation applied to a pressure-driven base flow in a meandering microchannel geometry. The electrical excitation induces a secondary electrokinetic velocity component which results in a complex flow field within the meander bends. A mathematical model describing the physicochemical phenomena present within the micromixer is implemented in an in-house Finite-Element-Method code. We first perform simulations comparable to experiments concerned with the investigation of the flow field in the bends. The comparison of simulation and experiment reveals excellent agreement. Hence, the validated model and numerical schemes are employed for a numerical optimization of the micromixer performance. In detail, we optimize the secondary electrokinetic flow by finding the best electrical excitation parameters, i.e. frequency and amplitude, for a given waveform. The simulation results of two optimized electrical excitations featuring a discrete and a continuous waveform are compared and discussed. The results demonstrate that the micromixer is able to achieve high mixing degrees very rapidly

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

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

Effect of grazing and mowing on the clonal structure of Elytrigia atherica: a long-term study of abandoned and managed sites

Physical disturbance by large herbivores can affect species diversity at the community level and concurrently genetic diversity at the species level. As seedling establishment is rarely observed in clonal plants, short-term experiments and demographic studies are unlikely to reveal the response of clonal plants to disturbances. A long-term (30-year) field experiment and the availability of molecularmarkers allowed us to investigate the clonal structure of populations of Elytrigia atherica subjected to different management regimes. The long-term field study provided us with five replicated blocks that had been subjected to three different management regimes, grazing by cattle, mowing and abandonment. In this study we examined the effects of herbivore grazing andmowing on clonal richness and genetic diversity of populations in salt marshes using multilocus microsatellite genotypes. In addition, phenotypic traits and spatial positions of E. atherica ramets were determined for 20 samples in a 5 × 10m plot in each of the blocks. Abundance and phenotypic traits were affected by the management regimes, resulting in a higher abundance in abandoned fields and plants having shorter and narrower leaves in managed fields. Biomass removal did affect the clonal structure of populations and increased the genetic diversity compared to that in abandoned fields. However, no distinct difference was found between the two management regimes, mowing and grazing. Although seedling recruitment has rarely been observed, the present study shows that such rare events have occurred within the populations studied. Thus, molecular tools can greatly increase our understanding of vegetation dynamics and processes within populations growing under different conditions

Electron-Phonon Interacation in Quantum Dots: A Solvable Model

The relaxation of electrons in quantum dots via phonon emission is hindered by the discrete nature of the dot levels (phonon bottleneck). In order to clarify the issue theoretically we consider a system of $N$ discrete fermionic states (dot levels) coupled to an unlimited number of bosonic modes with the same energy (dispersionless phonons). In analogy to the Gram-Schmidt orthogonalization procedure, we perform a unitary transformation into new bosonic modes. Since only $N(N+1)/2$ of them couple to the fermions, a numerically exact treatment is possible. The formalism is applied to a GaAs quantum dot with only two electronic levels. If close to resonance with the phonon energy, the electronic transition shows a splitting due to quantum mechanical level repulsion. This is driven mainly by one bosonic mode, whereas the other two provide further polaronic renormalizations. The numerically exact results for the electron spectral function compare favourably with an analytic solution based on degenerate perturbation theory in the basis of shifted oscillator states. In contrast, the widely used selfconsistent first-order Born approximation proves insufficient in describing the rich spectral features.Comment: 8 pages, 4 figure

Inelastic tunneling in a double quantum dot coupled to a bosonic environment

Coupling a quantum system to a bosonic environment always give rise to inelastic processes, which reduce the coherency of the system. We measure energy dependent rates for inelastic tunneling processes in a fully controllable two-level system of a double quantum dot. The emission and absorption rates are well repro-duced by Einstein's coefficients, which relate to the spontaneous emission rate. The inelastic tunneling rate can be comparable to the elastic tunneling rate if the boson occupation number becomes large. In the specific semiconductor double dot, the energy dependence of the inelastic rate suggests that acoustic phonons are coupled to the double dot piezoelectrically.Comment: 6 pages, 4 figure