Unzipping DNA with Optical Tweezers: High Sequence Sensitivity and Force Flips

AbstractForce measurements are performed on single DNA molecules with an optical trapping interferometer that combines subpiconewton force resolution and millisecond time resolution. A molecular construction is prepared for mechanically unzipping several thousand-basepair DNA sequences in an in vitro configuration. The force signals corresponding to opening and closing the double helix at low velocity are studied experimentally and are compared to calculations assuming thermal equilibrium. We address the effect of the stiffness on the basepair sensitivity and consider fluctuations in the force signal. With respect to earlier work performed with soft microneedles, we obtain a very significant increase in basepair sensitivity: presently, sequence features appearing at a scale of 10 basepairs are observed. When measured with the optical trap the unzipping force exhibits characteristic flips between different values at specific positions that are determined by the base sequence. This behavior is attributed to bistabilities in the position of the opening fork; the force flips directly reflect transitions between different states involved in the time-averaging of the molecular system

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

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

Seagrass wasting disease varies with salinity and depth in natural Zostera marina populations

In the 1930s the wasting disease pathogen Labyrinthula zosterae is believed to have killed 90% of the temperate seagrass Zostera marina in the Atlantic Ocean. Despite the devastating impact of this disease the host–pathogen interaction is still poorly understood, and few field studies have investigated factors correlating with the prevalence and abundance of L. zosterae. This study measures wasting disease in natural populations of Z. marina, showing a strong correlation between the disease and both salinity and water depth. No infection was detected in Z. marina shoots from low salinity (13–25 PSU) meadows, whereas most shoots carried the disease in high salinity (25–29 PSU). Shallow (1 m) living Z. marina shoots were also more infected compared to shoots in deeper (5 m) meadows. In addition, infection and transplantation experiments showed that Z. marina shoots from low salinity meadows with low pathogen pressure were more susceptible to L. zosterae infection. The higher susceptibility could not be explained by lower content of inhibitory defense compounds in the shoots. Instead, extracts from all Z. marina shoots significantly reduced pathogen growth, suggesting that Z. marina contains inhibitory compounds that function as a constitutive defense. Overall, the results show that seagrass wasting disease is common in natural Z. marina populations in the study area and that it increases with salinity and decreases with depth. Our findings also suggest that low salinity areas can act as a refuge against seagrass wasting disease

Multiband theory of multi-exciton complexes in self-assembled quantum dots

We report on a multiband microscopic theory of many-exciton complexes in self-assembled quantum dots. The single particle states are obtained by three methods: single-band effective-mass approximation, the multiband $k\cdot p$ method, and the tight-binding method. The electronic structure calculations are coupled with strain calculations via Bir-Pikus Hamiltonian. The many-body wave functions of $N$ electrons and $N$ valence holes are expanded in the basis of Slater determinants. The Coulomb matrix elements are evaluated using statically screened interaction for the three different sets of single particle states and the correlated $N$-exciton states are obtained by the configuration interaction method. The theory is applied to the excitonic recombination spectrum in InAs/GaAs self-assembled quantum dots. The results of the single-band effective-mass approximation are successfully compared with those obtained by using the of $k\cdot p$ and tight-binding methods.Comment: 10 pages, 8 figure

Non-equilibrium transport through a vertical quantum dot in the absence of spin-flip energy relaxation

We investigate non-equilibrium transport in the absence of spin-flip energy relaxation in a few-electron quantum dot artificial atom. Novel non-equilibrium tunneling processes involving high-spin states which cannot be excited from the ground state because of spin-blockade, and other processes involving more than two charge states are observed. These processes cannot be explained by orthodox Coulomb blockade theory. The absence of effective spin relaxation induces considerable fluctuation of the spin, charge, and total energy of the quantum dot. Although these features are revealed clearly by pulse excitation measurements, they are also observed in conventional dc current characteristics of quantum dots.Comment: accepted for publication in Phys. Rev.Let

Modulation of the Eelgrass – Labyrinthula zosterae Interaction Under Predicted Ocean Warming, Salinity Change and Light Limitation

Marine infectious diseases can have large-scale impacts when they affect foundation species such as seagrasses and corals. Interactions between host and disease, in turn, may be modulated by multiple perturbations associated with global change. A case in point is the infection of the foundation species Zostera marina (eelgrass) with endophytic net slime molds (Labyrinthula zosterae), the putative agent of eelgrass wasting disease that caused one of the most severe marine pandemics across the North-Atlantic in the 1930s. The contemporary presence of L. zosterae in many eelgrass meadows throughout Europe raises the question whether such a pandemic may re-appear if coastal waters become more eutrophic, warmer and less saline. Accordingly, we exposed uninfected Baltic Sea Z. marina plants raised from seeds to full factorial combinations of controlled L. zosterae inoculation, heat stress, light limitation (mimicking one consequence of eutrophication) and two salinity levels. We followed eelgrass wasting disease dynamics, along with several eelgrass responses such as leaf growth, mortality and carbohydrate storage, as well as the ability of plants to chemically inhibit L. zosterae growth. Contrary to our expectation, inoculation with L. zosterae reduced leaf growth and survival only under the most adverse condition to eelgrass (reduced light and warm temperatures). We detected a strong interaction between salinity and temperature on L. zosterae abundance and pathogenicity. The protist was unable to infect eelgrass under high temperature (27°C) in combination with low salinity (12 psu). With the exception of a small positive effect of temperature alone, no further effects of any of the treatment combinations on the defense capacity of eelgrass against L. zosterae were detectable. This work supports the idea that contemporary L. zosterae isolates neither represent an immediate risk for eelgrass beds in the Baltic Sea, nor a future one under the predicted salinity decrease and warming of the Baltic Sea