Forces and conductances in a single-molecule bipyridine junction

Inspired by recent measurements of forces and conductances of bipyridine nano-junctions, we have performed density functional theory calculations of structure and electron transport in a bipyridine molecule attached between gold electrodes for seven different contact geometries. The calculations show that both the bonding force and the conductance are sensitive to the surface structure, and that both properties are in good agreement with experiment for contact geometries characterized by intermediate coordination of the metal atoms corresponding to a stepped surface. The conductance is mediated by the lowest unoccupied molecular orbital, which can be illustrated by a quantitative comparison with a one-level model. Implications for the interpretation of the experimentally determined force and conductance distributions are discussed

Phylogenetic analysis accounting for age-dependent death and sampling with applications to epidemics

The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge, none of the epidemiological models currently used in phylogenetics can account for recovery rates and sampling rates dependent on the time elapsed since transmission. Here we introduce an epidemiological model where infectives leave the epidemic, either by recovery or sampling, after some random time which may follow an arbitrary distribution. We derive an expression for the likelihood of the phylogenetic tree of sampled infectives under our general epidemiological model. The analytic concept developed in this paper will facilitate inference of past epidemiological dynamics and provide an analytical framework for performing very efficient simulations of phylogenetic trees under our model. The main idea of our analytic study is that the non-Markovian epidemiological model giving rise to phylogenetic trees growing vertically as time goes by, can be represented by a Markovian "coalescent point process" growing horizontally by the sequential addition of pairs of coalescence and sampling times. As examples, we discuss two special cases of our general model, namely an application to influenza and an application to HIV. Though phrased in epidemiological terms, our framework can also be used for instance to fit macroevolutionary models to phylogenies of extant and extinct species, accounting for general species lifetime distributions.Comment: 30 pages, 2 figure

Towards Grower-friendly Apple Crop Thinning by Tree Shading

Light management with shading nets, which reduce sunlight by 74%, might be an alternative to chemicals commonly used for thinning on apple trees. To study the effect of shading on crop load and fruit quality, trials were conducted in field experiments with the cultivars Golden Delicious and Elstar in 2006. Trees were either covered 25 days after full bloom (DAFB) with a net during three days, or until the peak of fruit fall, observed after seven days shading. Ideal time length for optimal crop yield was seven days shading for Elstar and three days shading for Golden Delicious. Alternate bearing could be decreased as flower initiation counts the following year showed. In both experiments, inner quality of fruit such as sugar and firmness showed good values at optimal shading duration compared with chemical + hand thinning. In 2007, a second field trial was conducted with cultivars Golden Delicious and Topaz to study the time period for shading in further detail. Shading was done for three days at 19, 26 and 33 DAFB using two net types (three- and two-meter-net width, covering the trees entirely or only down to 50 cm above ground). For Golden Delicious, shading after 19 and 26 days reduced fruits per 100 flower cluster to the same extent as with chemical + hand thinning. There was no difference between the two net types. For Topaz, shading after 19 days showed the best results. Regarding inner quality of both cultivars, only sugar content for Golden Delicious could be significantly improved after 19 and 26 days shading. Further analyses are still under way (e.g. for acidity). This study is part of an effort for increasing European consumption with fruit from sustainable production systems, the ISAFRUIT-EU-project