Labyrinthine Island Growth during Pd/Ru(0001) Heteroepitaxy

Using low energy electron microscopy we observe that Pd deposited on Ru only attaches to small sections of the atomic step edges surrounding Pd islands. This causes a novel epitaxial growth mode in which islands advance in a snakelike motion, giving rise to labyrinthine patterns. Based on density functional theory together with scanning tunneling microscopy and low energy electron microscopy we propose that this growth mode is caused by a surface alloy forming around growing islands. This alloy gradually reduces step attachment rates, resulting in an instability that favors adatom attachment at fast advancing step sections

Fast coarsening in unstable epitaxy with desorption

Homoepitaxial growth is unstable towards the formation of pyramidal mounds when interlayer transport is reduced due to activation barriers to hopping at step edges. Simulations of a lattice model and a continuum equation show that a small amount of desorption dramatically speeds up the coarsening of the mound array, leading to coarsening exponents between 1/3 and 1/2. The underlying mechanism is the faster growth of larger mounds due to their lower evaporation rate.Comment: 4 pages, 4 PostScript figure

An ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis

Synthesis of acetate from carbon dioxide and molecular hydrogen is considered to be the first carbon assimilation pathway on earth. It combines carbon dioxide fixation into acetyl-CoA with the production of ATP via an energized cell membrane. How the pathway is coupled with the net synthesis of ATP has been an enigma. The anaerobic, acetogenic bacterium Acetobacterium woodii uses an ancient version of this pathway without cytochromes and quinones. It generates a sodium ion potential across the cell membrane by the sodium-motive ferredoxin:NAD oxidoreductase (Rnf). The genome sequence of A. woodii solves the enigma: it uncovers Rnf as the only ion-motive enzyme coupled to the pathway and unravels a metabolism designed to produce reduced ferredoxin and overcome energetic barriers by virtue of electron-bifurcating, soluble enzymes

Corrigendum: Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Peer Reviewe

Genome-Wide Association Studies for the Detection of Genetic Variants Associated With Daptomycin and Ceftaroline Resistance in Staphylococcus aureus

Background: As next generation sequencing (NGS) technologies have experienced a rapid development over the last decade, the investigation of the bacterial genetic architecture reveals a high potential to dissect causal loci of antibiotic resistance phenotypes. Although genome-wide association studies (GWAS) have been successfully applied for investigating the basis of resistance traits, complex resistance phenotypes have been omitted so far. For S. aureus this especially refers to antibiotics of last resort like daptomycin and ceftaroline. Therefore, we aimed to perform GWAS for the identification of genetic variants associated with DAP and CPT resistance in clinical S. aureus isolates. Materials/methods: To conduct microbial GWAS, we selected cases and controls according to their clonal background, date of isolation, and geographical origin. Association testing was performed with PLINK and SEER analysis. By using in silico analysis, we also searched for rare genetic variants in candidate loci that have previously been described to be involved in the development of corresponding resistance phenotypes. Results: GWAS revealed MprF P314L and L826F to be significantly associated with DAP resistance. These mutations were found to be homogenously distributed among clonal lineages suggesting convergent evolution. Additionally, rare and yet undescribed single nucleotide polymorphisms could be identified within mprF and putative candidate genes. Finally, we could show that each DAP resistant isolate exhibited at least one amino acid substitution within the open reading frame of mprF. Due to the presence of strong population stratification, no genetic variants could be associated with CPT resistance. However, the investigation of the staphylococcal cassette chromosome mec (SCCmec) revealed various mecA SNPs to be putatively linked with CPT resistance. Additionally, some CPT resistant isolates revealed no mecA mutations, supporting the hypothesis that further and still unknown resistance determinants are crucial for the development of CPT resistance in S. aureus. Conclusion: We hereby confirmed the potential of GWAS to identify genetic variants that are associated with antibiotic resistance traits in S. aureus. However, precautions need to be taken to prevent the detection of spurious associations. In addition, the implementation of different approaches is still essential to detect multiple forms of variations and mutations that occur with a low frequency.Peer Reviewe

Low-Energy Electron Microscopy Studies of Interlayer Mass Transport Kinetics on TiN(111)

In situ low-energy electron microscopy was used to study interlayer mass transport kinetics during annealing of three-dimensional (3D) TiN(111) mounds, consisting of stacked 2D islands, at temperatures T between 1550 and 1700 K. At each T, the islands decay at a constant rate, irrespective of their initial position in the mounds, indicating that mass is not conserved locally. From temperature-dependent island decay rates, we obtain an activation energy of 2.8+/-0.3 eV. This is consistent with the detachment-limited decay of 2D TiN islands on atomically-flat TiN(111) terraces [Phys. Rev. Lett. 89 (2002) 176102], but significantly smaller than the value, 4.5+/-0.2 eV, obtained for bulk-diffusion-limited spiral step growth [Nature 429, 49 (2004)]. We model the process based upon step flow, while accounting for step-step interactions, step permeability, and bulk mass transport. The results show that TiN(111) steps are highly permeable and exhibit strong repulsive temperature-dependent step-step interactions that vary between 0.003 and 0.076 eV-nm. The rate-limiting process controlling TiN(111) mound decay is surface, rather than bulk, diffusion in the detachment-limited regime.Comment: 26 pages, 5 figure

Atomic step motion during the dewetting of ultra-thin films

We report on three key processes involving atomic step motion during the dewetting of thin solid films: (i) the growth of an isolated island nucleated far from a hole, (ii) the spreading of a monolayer rim, and (iii) the zipping of a monolayer island along a straight dewetting front. Kinetic Monte Carlo results are in good agreement with simple analytical models assuming diffusion-limited dynamics.Comment: 7 pages, 5 figure

Coarsening of Surface Structures in Unstable Epitaxial Growth

We study unstable epitaxy on singular surfaces using continuum equations with a prescribed slope-dependent surface current. We derive scaling relations for the late stage of growth, where power law coarsening of the mound morphology is observed. For the lateral size of mounds we obtain $\xi \sim t^{1/z}$ with $z \geq 4$. An analytic treatment within a self-consistent mean-field approximation predicts multiscaling of the height-height correlation function, while the direct numerical solution of the continuum equation shows conventional scaling with z=4, independent of the shape of the surface current.Comment: 15 pages, Latex. Submitted to PR

Factors influencing graphene growth on metal surfaces

Graphene forms from a relatively dense, tightly-bound C-adatom gas, when elemental C is deposited on or segregates to the Ru(0001) surface. Nonlinearity of the graphene growth rate with C adatom density suggests that growth proceeds by addition of C atom clusters to the graphene edge. The generality of this picture has now been studied by use of low-energy electron microscopy (LEEM) to observe graphene formation when Ru(0001) and Ir(111) surfaces are exposed to ethylene. The finding that graphene growth velocities and nucleation rates on Ru have precisely the same dependence on adatom concentration as for elemental C deposition implies that hydrocarbon decomposition only affects graphene growth through the rate of adatom formation; for ethylene, that rate decreases with increasing adatom concentration and graphene coverage. Initially, graphene growth on Ir(111) is like that on Ru: the growth velocity is the same nonlinear function of adatom concentration (albeit with much smaller equilibrium adatom concentrations, as we explain with DFT calculations of adatom formation energies). In the later stages of growth, graphene crystals that are rotated relative to the initial nuclei nucleate and grow. The rotated nuclei grow much faster. This difference suggests first, that the edge-orientation of the graphene sheets relative to the substrate plays an important role in the growth mechanism, and second, that attachment of the clusters to the graphene is the slowest step in cluster addition, rather than formation of clusters on the terraces