Draft Genome Sequence of the Biocontrol Strain Serratia plymuthica A30, Isolated from Rotting Potato Tuber Tissue

Serratia plymuthica A30 is a Gram-negative bacterium expressing antagonistic activity toward blackleg- and soft rot-causing Dickeya sp. biovar 3 (“Dickeya solani”). Here, we present the draft genome sequence of strain A30, which has been isolated from rotten potato tuber tissu

A new type of reconstruction on the InSb() surface determined by grazing incidence X-ray diffraction

The (3×3) reconstruction of the InSb( ) surface has been investigated by grazing incidence X-ray diffraction and scanning tunneling microscopy. The structure is characterized by 6-atom rings on top of a slightly buckled InSb top double layer. Two types of rings have been found, an elliptic ring consisting of 4 In and 2 Sb atoms and a trigonal ring with 3 In and 3 Sb atoms. The bond angles and lengths are consistent with the concept of rehybridization and depolarization which explains the reconstructions of the (111) and (110) surfaces

Mounding Instability and Incoherent Surface Kinetics

Mounding instability in a conserved growth from vapor is analysed within the framework of adatom kinetics on the growing surface. The analysis shows that depending on the local structure on the surface, kinetics of adatoms may vary, leading to disjoint regions in the sense of a continuum description. This is manifested particularly under the conditions of instability. Mounds grow on these disjoint regions and their lateral growth is governed by the flux of adatoms hopping across the steps in the downward direction. Asymptotically ln(t) dependence is expected in 1+1- dimensions. Simulation results confirm the prediction. Growth in 2+1- dimensions is also discussed.Comment: 4 pages, 4 figure

Surface Kinetics and Generation of Different Terms in a Conservative Growth Equation

A method based on the kinetics of adatoms on a growing surface under epitaxial growth at low temperature in (1+1) dimensions is proposed to obtain a closed form of local growth equation. It can be generalized to any growth problem as long as diffusion of adatoms govern the surface morphology. The method can be easily extended to higher dimensions. The kinetic processes contributing to various terms in the growth equation (GE) are identified from the analysis of in-plane and downward hops. In particular, processes corresponding to the (h -> -h) symmetry breaking term and curvature dependent term are discussed. Consequence of these terms on the stable and unstable transition in (1+1) dimensions is analyzed. In (2+1) dimensions it is shown that an additional (h -> -h) symmetry breaking term is generated due to the in-plane curvature associated with the mound like structures. This term is independent of any diffusion barrier differences between in-plane and out of-plane migration. It is argued that terms generated in the presence of downward hops are the relevant terms in a GE. Growth equation in the closed form is obtained for various growth models introduced to capture most of the processes in experimental Molecular Beam Epitaxial growth. Effect of dissociation is also considered and is seen to have stabilizing effect on the growth. It is shown that for uphill current the GE approach fails to describe the growth since a given GE is not valid over the entire substrate.Comment: 14 pages, 7 figure

Strategic investment explains patterns of cooperation and cheating in a microbe

Contributing to cooperation is typically costly, while its rewards are often available to all members of a social group. So why should individuals be willing to pay these costs, especially if they could cheat by exploiting the investments of others? Kin selection theory broadly predicts that individuals should invest more into cooperation if their relatedness to group members is high (assuming they can discriminate kin from nonkin). To better understand how relatedness affects cooperation, we derived the ‟Collective Investment" game, which provides quantitative predictions for patterns of strategic investment depending on the level of relatedness. We then tested these predictions by experimentally manipulating relatedness (genotype frequencies) in mixed cooperative aggregations of the social amoeba Dictyostelium discoideum, which builds a stalk to facilitate spore dispersal. Measurements of stalk investment by natural strains correspond to the predicted patterns of relatedness-dependent strategic investment, wherein investment by a strain increases with its relatedness to the group. Furthermore, if overall group relatedness is relatively low (i.e., no strain is at high frequency in a group) strains face a scenario akin to the "Prisoner's Dilemma" and suffer from insufficient collective investment. We find that strains employ relatedness-dependent segregation to avoid these pernicious conditions. These findings demonstrate that simple organisms like D. discoideum are not restricted to being ‟cheaters" or ‟cooperators" but instead measure their relatedness to their group and strategically modulate their investment into cooperation accordingly. Consequently, all individuals will sometimes appear to cooperate and sometimes cheat due to the dynamics of strategic investing

M-theory on `toric' G_2 cones and its type II reduction

We analyze a class of conical G_2 metrics admitting two commuting isometries, together with a certain one-parameter family of G_2 deformations which preserves these symmetries. Upon using recent results of Calderbank and Pedersen, we write down the explicit G_2 metric for the most general member of this family and extract the IIA reduction of M-theory on such backgrounds, as well as its type IIB dual. By studying the asymptotics of type II fields around the relevant loci, we confirm the interpretation of such backgrounds in terms of localized IIA 6-branes and delocalized IIB 5-branes. In particular, we find explicit, general expressions for the string coupling and R-R/NS-NS forms in the vicinity of these objects. Our solutions contain and generalize the field configurations relevant for certain models considered in recent work of Acharya and Witten.Comment: 45 pages, references adde

Unconventional MBE Strategies from Computer Simulations for Optimized Growth Conditions

We investigate the influence of step edge diffusion (SED) and desorption on Molecular Beam Epitaxy (MBE) using kinetic Monte-Carlo simulations of the solid-on-solid (SOS) model. Based on these investigations we propose two strategies to optimize MBE growth. The strategies are applicable in different growth regimes: During layer-by-layer growth one can exploit the presence of desorption in order to achieve smooth surfaces. By additional short high flux pulses of particles one can increase the growth rate and assist layer-by-layer growth. If, however, mounds are formed (non-layer-by-layer growth) the SED can be used to control size and shape of the three-dimensional structures. By controlled reduction of the flux with time we achieve a fast coarsening together with smooth step edges.Comment: 19 pages, 7 figures, submitted to Phys. Rev.

Intersecting 6-branes from new 7-manifolds with G_2 holonomy

We discuss a new family of metrics of 7-manifolds with G_2 holonomy, which are R^3 bundles over a quaternionic space. The metrics depend on five parameters and have two Abelian isometries. Certain singularities of the G_2 manifolds are related to fixed points of these isometries; there are two combinations of Killing vectors that possess co-dimension four fixed points which yield upon compactification only intersecting D6-branes if one also identifies two parameters. Two of the remaining parameters are quantized and we argue that they are related to the number of D6-branes, which appear in three stacks. We perform explicitly the reduction to the type IIA model.Comment: 25 pages, 1 figure, Latex, small changes and add refs, version appeared in JHE

Probing the close environment of young stellar objects with interferometry

The study of Young Stellar Objects (YSOs) is one of the most exciting topics that can be undertaken by long baseline optical interferometry. The magnitudes of these objects are at the edge of capabilities of current optical interferometers, limiting the studies to a few dozen, but are well within the capability of coming large aperture interferometers like the VLT Interferometer, the Keck Interferometer, the Large Binocular Telescope or 'OHANA. The milli-arcsecond spatial resolution reached by interferometry probes the very close environment of young stars, down to a tenth of an astronomical unit. In this paper, I review the different aspects of star formation that can be tackled by interferometry: circumstellar disks, multiplicity, jets. I present recent observations performed with operational infrared interferometers, IOTA, PTI and ISI, and I show why in the next future one will extend these studies with large aperture interferometers.Comment: Review to be published in JENAM'2002 proceedings "The Very Large Telescope Interferometer Challenges for the future

A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer

We introduce a Markov model for the evolution of a gene family along a phylogeny. The model includes parameters for the rates of horizontal gene transfer, gene duplication, and gene loss, in addition to branch lengths in the phylogeny. The likelihood for the changes in the size of a gene family across different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space, where N is the number of organisms, $h$ is the height of the phylogeny, and M is the sum of family sizes. We apply the model to the evolution of gene content in Preoteobacteria using the gene families in the COG (Clusters of Orthologous Groups) database