Degradation of RNA in bacteria: comparison of mRNA and stable RNA

Degradation of RNA plays a central role in RNA metabolism. In recent years, our knowledge of the mechanisms of RNA degradation has increased considerably with discovery of the participating RNases and analysis of mutants affected in the various degradative pathways. Among these processes, mRNA decay and stable RNA degradation generally have been considered distinct, and also separate from RNA maturation. In this review, each of these processes is described, as it is currently understood in bacteria. The picture that emerges is that decay of mRNA and degradation of stable RNA share many common features, and that their initial steps also overlap with those of RNA maturation. Thus, bacterial cells do not contain dedicated machinery for degradation of different classes of RNA or for different processes. Rather, only the specificity of the RNase and the accessibility of the substrate determine whether or not a particular RNA will be acted upon

Localization and superconducting proximity effect in sandwiched potassium films

Thin films of alkali metals when sandwiched at both surfaces by thin metal films loose their conductance. The superconducting proximity effect is used to investigate the change in the alkali film. On the length scale of the film thickness the electronic properties of the alkali film do not change noticeably although its conductance is dramatically reduced, corresponding to localized electrons.Comment: 13 pages, 5 figure

Superconducting proximity effects in metals with a repulsive pairing interaction

Studies of the superconducting proximity effect in normal conductor/superconductor $(N/S)$ junctions almost universally assume no effective electron-electron coupling in the $N$ region. While such an approximation leads to a simple description of the proximity effect, it is unclear how it could be rigorously justified. We reveal a much more complex picture of the proximity effect in $N/S$ bilayers, where $S$ is a clean s-wave BCS superconductor and $N$ is a simple metal with a repulsive effective electron coupling. We elucidate the proximity effect behavior using a highly accurate method to self-consistently solve the Bogoliubov-deGennes equations. We present our results for a wide range of values of the interface scattering, the Fermi wave vector mismatch, the temperature, and the ratio $g$ of the effective interaction strengths in the $N$ and $S$ region. We find that the repulsive interaction, represented by a negative $g$, strongly alters the signatures of the proximity effect as can be seen in the spatial dependence of the Cooper pair amplitude and the pair potential, as well as in the local density of states near the interface.Comment: 12 pages, including 10 figures. To appear in Phys. Rev.

Characteristic energies, transition temperatures, and switching effects in clean SNS graphene nanostructures

We study proximity effects in clean nanoscale superconductor-normal metal-superconductor (S$\mid$N$\mid$S) graphene heterostructures using a self-consistent numerical solution to the continuum Dirac Bogoliubov-de Gennes (DBdG) equations. We obtain results for the pair amplitude and the local density of states (DOS), as a function of doping and of the geometrical parameters determining the width of the structures. The superconducting correlations are found to penetrate the normal graphene layers even when there is extreme mismatch in the normal and superconducting doping levels, where specular Andreev reflection dominates. The local DOS exhibits peculiar features, which we discuss, arising from the Dirac cone dispersion relation and from the interplay between the superconducting and Thouless energy scales. The corresponding characteristic energies emerge in the form of resonant peaks in the local DOS, that depend strongly on the doping level, as does the energy gap, which declines sharply as the relative difference in doping between the S and N regions is reduced. We also linearize the DBdG equations and develop an essentially analytical method that determines the critical temperature $T_c$ of an \sns nanostructure self-consistently. We find that for S regions that occupy a fraction of the coherence length, $T_c$ can undergo substantial variations as a function of the relative doping. At finite temperatures and by manipulating the doping levels, the self consistent pair amplitudes reveal dramatic transitions between a superconducting and resistive normal state of the structure. Such behavior suggests the possibility of using the proposed system as a carbon-based superconducting switch, turning superconductivity on or off by tuning the relative doping levels.Comment: 13 pages, figures include

Quantitative Simulation of the Superconducting Proximity Effect

A numerical method is developed to calculate the transition temperature of double or multi-layers consisting of films of super- and normal conductors. The approach is based on a dynamic interpretation of Gorkov's linear gap equation and is very flexible. The mean free path of the different metals, transmission through the interface, ratio of specular reflection to diffusive scattering at the surfaces, and fraction of diffusive scattering at the interface can be included. Furthermore it is possible to vary the mean free path and the BCS interaction NV in the vicinity of the interface. The numerical results show that the normalized initial slope of an SN double layer is independent of almost all film parameters except the ratio of the density of states. There are only very few experimental investigations of this initial slope and they consist of Pb/Nn double layers (Nn stands for a normal metal). Surprisingly the coefficient of the initial slope in these experiments is of the order or less than 2 while the (weak coupling) theory predicts a value of about 4.5. This discrepancy has not been recognized in the past. The autor suggests that it is due to strong coupling behavior of Pb in the double layers. The strong coupling gap equation is evaluated in the thin film limit and yields the value of 1.6 for the coefficient. This agrees much better with the few experimental results that are available. PACS: 74.45.+r, 74.62.-c, 74.20.F

Towards understanding the variability in biospheric CO2 fluxes:Using FTIR spectrometry and a chemical transport model to investigate the sources and sinks of carbonyl sulfide and its link to CO2

Understanding carbon dioxide (CO2) biospheric processes is of great importance because the terrestrial exchange drives the seasonal and interannual variability of CO2 in the atmosphere. Atmospheric inversions based on CO2 concentration measurements alone can only determine net biosphere fluxes, but not differentiate between photosynthesis (uptake) and respiration (production). Carbonyl sulfide (OCS) could provide an important additional constraint: it is also taken up by plants during photosynthesis but not emitted during respiration, and therefore is a potential means to differentiate between these processes. Solar absorption Fourier Transform InfraRed (FTIR) spectrometry allows for the retrievals of the atmospheric concentrations of both CO2 and OCS from measured solar absorption spectra. Here, we investigate co-located and quasi-simultaneous FTIR measurements of OCS and CO2 performed at five selected sites located in the Northern Hemisphere. These measurements are compared to simulations of OCS and CO2 using a chemical transport model (GEOS-Chem). The coupled biospheric fluxes of OCS and CO2 from the simple biosphere model (SiB) are used in the study. The CO2 simulation with SiB fluxes agrees with the measurements well, while the OCS simulation reproduced a weaker drawdown than FTIR measurements at selected sites, and a smaller latitudinal gradient in the Northern Hemisphere during growing season when comparing with HIPPO (HIAPER Pole-to-Pole Observations) data spanning both hemispheres. An offset in the timing of the seasonal cycle minimum between SiB simulation and measurements is also seen. Using OCS as a photosynthesis proxy can help to understand how the biospheric processes are reproduced in models and to further understand the carbon cycle in the real world

Transport properties of ybco thin films near the critical state with no applied field

Transport measurements carried out on twinned ybco films are compared to the predictions of a previously proposed model suggesting that the vortices move along the films twin boundaries that behave as rows of Josephson weak links [P.Bernstein and J.F.Hamet, J.Appl.Phys.95 (2004) 2569]. The obtained results suggest that, except if the films are very thin, the twin boundaries consist of superimposed rows of weak links with mean height,ds, whose mean length along the TBs is an universal function of T/Tc, the reduced temperature. This conclusion yields a general expression for the critical surface current density of the films as a function of T/Tc and of the number of superimposed weak links rows, while the critical current density depends on ds. A comparison of the measurements reported by various authors shows that the nature of the substrate and the growth technique have both a strong effect on ds . The existence of superimposed weak links rows is attributed to extended defects generated by y2o3 inclusions.Comment: 33 pages, 13 figures; accepted for publication in Physica

Inter- and Intragranular Effects in Superconducting Compacted Platinum Powders

Compacted platinum powders exhibit a sharp onset of diamagnetic screening at $T \simeq 1.9$ mK in zero magnetic field in all samples investigated. This sharp onset is interpreted in terms of the intragranular transition into the superconducting state. At lower temperatures, the magnetic ac susceptibility strongly depends on the ac field amplitude and reflects the small intergranular critical current density $j_{c}$. This critical current density shows a strong dependence on the packing fraction f of the granular samples. Surprisingly, $j_{c}$ increases significantly with decreasing f ($j_{c}(B=0, T=0) \simeq 0.07$ A/cm$^{2}$ for f = 0.67 and $j_{c}(B=0, T=0) \simeq 0.8$ A/cm$^{2}$ for f = 0.50). The temperature dependence of $j_{c}$ shows strong positive curvature over a wide temperature range for both samples. The phase diagrams of inter- and intragranular superconductivity for different samples indicate that the granular structure might play the key role for an understanding of the origin of superconductivity in the platinum compacts.Comment: 11 pages including 9 figures. To appear in Phys. Rev. B in Nov. 0