Formation of Turing structures in catalytic surface reactions: The facetting of Pt(110) in CO+O₂

The Pt(110) surface facets during the catalytic oxidation of CO, if reaction conditions are adjusted such that the CO‐induced 1×1⇄1×2 phase transition can take place simultaneously. A detailed low‐energy electron diffraction beam profile analysis revealed that regularly spaced (430) and (340) facets are formed with a lateral periodicity of ∼70 lattice units along the [11̄0] direction. This result, together with the observation that the facetted surface is only stable under reaction conditions, indicates a dissipative structure of the Turing type. Such structures, which are stationary but exhibit a periodic variation of the concentration variables in space, have so far almost exclusively been discussed theoretically. The interpretation of the facetted surface as a Turing structure could be confirmed by a Monte Carlo simulation based on the Langmuir Hinshelwood mechanism of catalytic CO oxidation and the CO‐induced 1×1⇄1×2 phase transition

Rigidity analysis of HIV-1 protease

We present a rigidity analysis on a large number of X-ray crystal structures of the enzyme HIV-1 protease using the 'pebble game' algorithm of the software FIRST. We find that although the rigidity profile remains similar across a comprehensive set of high resolution structures, the profile changes significantly in the presence of an inhibitor. Our study shows that the action of the inhibitors is to restrict the flexibility of the beta-hairpin flaps which allow access to the active site. The results are discussed in the context of full molecular dynamics simulations as well as data from NMR experiments.Comment: 4 pages, 3 figures. Conference proceedings for CMMP conference 2010 which was held at the University of Warwic

Surface Morphology and Strain Relief in Surfactant Mediated Growth of Germanium on Silicon (111)

The growth of Ge on Si is strongly modified by adsorbates called surfactants. The relevance of the stress on surface morphology and the growth mode of Ge on Si(111) is presented in a detailed in situ study by high resolution low energy electron diffraction (LEED) during the deposition. The change from islanding to layer-by-layer growth mode is seen in the oscillatory intensity behaviour of the 00-spot. As a strain relief mechanism, the Ge-film forms a microscopic rough surface of small triangular and defect-free pyramids in the pseudomorphic growth regime up to 8 monolayers. As soon as the pyramids are completed and start to coalesce, strain relieving defects are created at their base, finally arranging to the dislocation network. Without the driving force for the micro-roughness, the stress, the surface flattens again showing a much larger terrace length. The formation process of the dislocation network results in a spot splitting in LEED, since the periodic dislocations at the interface give rise to elastic deformation of the surface. Surprisingly the Ge-film is relaxed to 70% immediately after 8 monolayers of coverage, which is attributed to the micro rough surface morphology, providing innumerous nucleation sites for dislocation

A transmission x ray microscopy and NEXAFS approach for studying corroded silicate glasses at the nanometre scale

In this study transmission X ray microscopy TXM was tested as a method to investigate the chemistry and structure of corroded silicate glasses at the nanometer scale. Three different silicate glasses were altered in static corrosion experiments for 1 336 hours at temperatures between 60 C and 85 C using a 25 HCl solution. Thin lamellas were cut perpendicular to the surface of corroded glass monoliths and were analysed with conventional TEM as well as with TXM. By recording optical density profiles at photon energies around the Na and O K edges, the shape of the corrosion rim pristine glass interfaces and the thickness of the corrosion rims has been determined. Na and O near edge X ray absorption fine structure spectra NEXAFS were obtained without inducing irradiation damage and have been used to detect chemical changes in the corrosion rims. Spatially resolved NEXAFS spectra at the O K edge provided insight to structural changes in the corrosion layer on the atomic scale. By comparison to O K edge spectra of silicate minerals and hydrous albite glass as well as to O K edge NEXAFS of model structures simulated with ab initio calculations, evidence is provided that changes of the fine structure at the O K edge are assigned to the formation of siloxane groups in the corrosion ri

Anomalous thickness dependence of the Hall effect in ultrathin Pb layers on Si(111)

The magnetoconductive properties of ultrathin Pb films deposited on Si(111) are measured and compared with density-functional electronic band-structure calculations on two-dimensional, free-standing, 1 to 8 monolayers thick Pb(111) slabs. A description with free-standing slabs is possible because it turned out that the Hall coefficient is independent of the substrate and of the crystalline order in the film. We show that the oscillations in sign of the Hall coefficient observed as a function of film thickness can be explained directly from the thickness dependent variations of the electronic bandstructure at the Fermi energy.Comment: 4 pages incl. 3 figures, RevTeX, to appear in Phys. Rev.

A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells

In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: 1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone whose faces are determined empirically from a set of relations between the coordinates of the molecule, 2nd) it is also shown that this cone can be decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.Comment: added an intrduction and reference