Modeling contact formation between atomic-sized gold tips via molecular dynamics

The formation and rupture of atomic-sized contacts is modelled by means of molecular dynamics simulations. Such nano-contacts are realized in scanning tunnelling microscope and mechanically controlled break junction experiments. These instruments routinely measure the conductance across the nano-sized electrodes as they are brought into contact and separated, permitting conductance traces to be recorded that are plots of conductance versus the distance between the electrodes. One interesting feature of the conductance traces is that for some metals and geometric configurations a jump in the value of the conductance is observed right before contact between the electrodes, a phenomenon known as jump-to-contact. This paper considers, from a computational point of view, the dynamics of contact between two gold nano-electrodes. Repeated indentation of the two surfaces on each other is performed in two crystallographic orientations of face-centred cubic gold, namely (001) and (111). Ultimately, the intention is to identify the structures at the atomic level at the moment of first contact between the surfaces, since the value of the conductance is related to the minimum cross-section in the contact region. Conductance values obtained in this way are determined using first principles electronic transport calculations, with atomic configurations taken from the molecular dynamics simulations serving as input structures.Comment: 6 pages, 4 figures, conference submissio

Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story.

Buchnera aphidicola, the primary endosymbiont of aphids, has undergone important genomic and biochemical changes as an adaptation to intracellular life. The most important structural changes include a drastic genome reduction and the amplification of genes encoding key enzymes for the biosynthesis of amino acids by their translocation to plasmids. Molecular characterization through different aphid subfamilies has revealed that the genes involved in leucine and tryptophan biosynthesis show a variable fate, since they can be located on plasmids or on the chromosome in different lineages. This versatility contrasts with the genomic stasis found in three distantly related B. aphidicola strains already sequenced. We present the analysis of three B. aphidicola strains (BTg, BCt and BCc) belonging to aphids from different tribes of the subfamily Lachninae, that was estimated to harbour the bacteria with the smallest genomes. The presence of both leucine and tryptophan plasmids in BTg, a chimerical leucine-tryptophan plasmid in BCt, and only a leucine plasmid in BCc, indicates the existence of many recombination events in a recA minus bacterium. In addition, these B. aphidicola plasmids are the simplest described in this species, indicating that plasmids are also involved in the genome shrinkage process

The cosmic evolution of radio-AGN feedback to z=1

This paper presents the first measurement of the radio luminosity function of 'jet-mode' (radiatively-inefficient) radio-AGN out to z=1, in order to investigate the cosmic evolution of radio-AGN feedback. Eight radio source samples are combined to produce a catalogue of 211 radio-loud AGN with 0.5<z<1.0, which are spectroscopically classified into jet-mode and radiative-mode (radiatively-efficient) AGN classes. Comparing with large samples of local radio-AGN from the Sloan Digital Sky Survey, the cosmic evolution of the radio luminosity function of each radio-AGN class is independently derived. Radiative-mode radio-AGN show an order of magnitude increase in space density out to z~1 at all luminosities, consistent with these AGN being fuelled by cold gas. In contrast, the space density of jet-mode radio-AGN decreases with increasing redshift at low radio luminosities (L_1.4 < 1e24 W/Hz) but increases at higher radio luminosities. Simple models are developed to explain the observed evolution. In the best-fitting models, the characteristic space density of jet-mode AGN declines with redshift in accordance with the declining space density of massive quiescent galaxies, which fuel them via cooling of gas in their hot haloes. A time delay of 1.5-2 Gyr may be present between the quenching of star formation and the onset of jet-mode radio-AGN activity. The behaviour at higher radio luminosities can be explained either by an increasing characteristic luminosity of jet-mode radio-AGN activity with redshift (roughly as (1+z) cubed) or if the jet-mode radio-AGN population also includes some contribution of cold-gas-fuelled sources seen at a time when their accretion rate was low. Higher redshifts measurements would distinguish between these possibilities.Comment: Accepted for publication in MNRA

The AMIGA sample of isolated galaxies: VIII. The rate of asymmetric HI profiles in spiral galaxies

(abridged) Measures of the HI properties of a galaxy are among the most sensitive interaction diagnostic at our disposal. We report here on a study of HI profile asymmetries (e.g., lopsidedness) in a sample of some of the most isolated galaxies in the local Universe. This presents us with an excellent opportunity to quantify the range of intrinsic HI asymmetries and provides us with a zero-point calibration for evaluating these measurements in less isolated samples. We characterize the HI profile asymmetries and search for correlations between HI asymmetry and their environments, as well as their optical and far infrared (FIR) properties. We use high signal-to-noise global HI profiles for galaxies in the AMIGA project (http://amiga.iaa.csic.es). We restrict our study to N=166 galaxies with accurate measures of the HI shape properties. We quantify asymmetries using a flux ratio parameter. The asymmetry parameter distribution of our isolated sample is well described by a Gaussian model. The width of the distribution is sigma=0.13, and could be even smaller (sigma=0.11) if instrumental errors are reduced. Only 2% of our carefully vetted isolated galaxies sample show an asymmetry in excess of 3sigma. By using this sample we minimize environmental effects as confirmed by the lack of correlation between HI asymmetry and tidal force (one-on-one interactions) and neighbor galaxy number density. On the other hand, field galaxy samples show wider distributions and deviate from a Gaussian curve. As a result we find higher asymmetry rates (~10-20%) in such samples. We find evidence that the spiral arm strength is inversely correlated with the HI asymmetry. We also find an excess of FIR luminous galaxies with larger HI asymmetries that may be spirals associated with hidden accretion events. Our sample presents the smallest fraction of asymmetric HI profiles compared with any other yet studied.Comment: 18 pages, 17 figures, accepted for publication in A&

Modelling the inorganic nitrogen behaviour in a small Mediterranean forested catchment, Fuirosos (Catalonia)

The aim of this work was to couple a nitrogen (N) sub-model to already existent hydrological lumped (LU4-N) and semi-distributed (LU4-R-N and SD4-R-N) conceptual models, to improve our understanding of the factors and processes controlling nitrogen cycling and losses in Mediterranean catchments. The N model adopted provides a simplified conceptualization of the soil nitrogen cycle considering mineralization, nitrification, immobilization, denitrification, plant uptake, and ammonium adsorption/desorption. It also includes nitrification and denitrification in the shallow perched aquifer. We included a soil moisture threshold for all the considered soil biological processes. The results suggested that all the nitrogen processes were highly influenced by the rain episodes and that soil microbial processes occurred in pulses stimulated by soil moisture increasing after rain. Our simulation highlighted the riparian zone as a possible source of nitrate, especially after the summer drought period, but it can also act as an important sink of nitrate due to denitrification, in particular during the wettest period of the year. The riparian zone was a key element to simulate the catchment nitrate behaviour. The lumped LU4-N model (which does not include the riparian zone) could not be validated, while both the semi-distributed LU4-R-N and SD4-R-N model (which include the riparian zone) gave satisfactory results for the calibration process and acceptable results for the temporal validation process