Spontaneous formation and stability of small GaP fullerenes

We report the spontaneous formation of a GaP fullerene cage in ab-initio Molecular Dynamics simulations starting from a bulk fragment. A systematic study of the geometric and electronic properties of neutral and ionized GaP clusters suggests the stability of hetero-fullerenes formed by a compound with zincblend bulk structure. We find that GaP fullerenes up to 28 atoms have high symmetry, closed electronic shells, large HOMO-LUMO energy gaps and do not dissociate when ionized. We compare our results for GaP with those obtained by other groups for the corresponding BN clusters.Comment: To appear on PRL, 4 pages, 1 figure, Late

Assessment of phenomenological models for viscosity of liquids based on nonequilibrium atomistic simulations of copper

The shear viscosity of liquid copper is studied using nonequilibrium molecular-dynamics simulations under planar shear flow conditions. We examined variation of viscosity as function of shear rate at a range of pressures (ca. 0 - 40 GPa). We analyzed these results using eight different phenomenological models and find that the observed non-Newtonian behavior is best described by the Powell-Eyring (PE) model: eta(gamma)=(eta(0)-eta(infinity))sinh(-1)(tau gamma)/(tau gamma)+eta(infinity), where gamma is the shear rate. Here eta(0) (the zero-shear-rate viscosity) extracted from the PE fit is in excellent agreement with available experimental data. The relaxation time tau from the PE fit describes the shear response to an applied stress. This provides the framework for interpreting the shear flow phenomena in complex systems, such as liquid metal and amorphous metal alloys

Mass extinctions and supernova explosions

A nearby supernova (SN) explosion could have negatively influenced life on Earth, maybe even been responsible for mass extinctions. Mass extinction poses a significant extinction of numerous species on Earth, as recorded in the paleontologic, paleoclimatic, and geological record of our planet. Depending on the distance between the Sun and the SN, different types of threats have to be considered, such as ozone depletion on Earth, causing increased exposure to the Sun's ultraviolet radiation, or the direct exposure of lethal x-rays. Another indirect effect is cloud formation, induced by cosmic rays in the atmosphere which result in a drop in the Earth's temperature, causing major glaciations of the Earth. The discovery of highly intensive gamma ray bursts (GRBs), which could be connected to SNe, initiated further discussions on possible life-threatening events in Earth's history. The probability that GRBs hit the Earth is very low. Nevertheless, a past interaction of Earth with GRBs and/or SNe cannot be excluded and might even have been responsible for past extinction events.Comment: Chapter for forthcoming book: Handbook of Supernovae, P. Murdin and A. Alsabeti (eds.), Springer International Publishing (in press

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing

Present-day cosmic abundances. A comprehensive study of nearby early B-type stars and implications for stellar and Galactic evolution and interstellar dust models

Aims. A sample of early B-type stars in OB associations and the field within the solar neighbourhood is studied comprehensively. Present-day abundances for the astrophysically most interesting chemical elements are derived. Methods. High-resolution and high-S/N spectra of early B-type stars are analysed in NLTE. Atmospheric parameters are derived from the simultaneous establishment of independent indicators, from multiple ionization equilibria and the hydrogen Balmer lines. Results. Teff is constrained to 1-2% and logg to less than 15% uncertainty. Absolute values for metal abundances are determined to better than 25% uncertainty. The synthetic spectra match the observations reliably over almost the entire visual spectral range. Conclusions. A present-day cosmic abundance standard is established. Our results i) resolve the discrepancy between a chemical homogeneous local gas-phase ISM and a chemically inhomogeneous young stellar component, ii) facilitate the amount of heavy elements locked up in the interstellar dust to be constrained precisely: carbonaceous dust is largely destroyed inside the Orion HII region, unlike the silicates, and that graphite is only a minority species in interstellar dust -, iii) show that the mixing of CNO-burning products in the course of massive star evolution follows tightly the predicted nuclear path, iv) provide reliable present-day reference points for anchoring Galactic chemical evolution models to observation, and v) imply that the Sun has migrated outwards from the inner Galactic disk over its lifetime from a birthplace at a distance around 5-6 kpc from the Galactic Centre; a cancellation of the effects of Galactic chemical evolution and abundance gradients leads to the similarity of solar and present-day cosmic abundances in the solar neighbourhood, with a telltaling signature of the Sun's origin left in the C/O ratio. (ABRIDGED)Comment: 20 pages, 11 figures, published in A&A. A complete version (57 pages, 17 figures) including online material can be downloaded from http://www.sternwarte.uni-erlangen.de/~nieva/8158.pd

Hydrocarbon and halocarbon measurements as photochemical and dynamical indicators of atmospheric hydroxyl, atomic chlorine, and vertical mixing obtained during Lagrangian flights

Nonmethane hydrocarbons and halocarbons were measured during two Lagrangian experiments conducted in the lower troposphere of the North Atlantic as part of the June 1992, Atlantic Stratosphere Transition Experiment/Marine Aerosol and Gas Exchange (ASTEX/MAGE) expedition. The first experiment was performed in very clean marine air. Meteorological observations indicate that the height of the marine boundary layer rose rapidly, entraining free tropospheric air. However, the free tropospheric and marine boundary layer halocarbon concentrations were too similar to allow this entrainment to be quantified by these measurements. The second Lagrangian experiment took place along the concentration gradient of an aged continental air mass advecting from Europe. The trace gas measurements confirm that the National Center for Atmospheric Research (NCAR) Electra aircraft successfully intercepted the same air mass on consecutive days. Two layers, a surface layer and a mixed layer with chemically distinct compositions, were present within the marine boundary layer. The composition of the free troposphere was very different from that of the mixed layer, making entrainment from the free troposphere evident Concentrations of the nonmethane hydrocarbons in the Lagrangian surface layer were observed to become depleted relative to the longer-lived tetrachloroethene. A best fit to the observations was calculated using various combinations of the three parameters, loss by reaction with hydroxyl, loss by reaction with chlorine, and/or dilution from the mixed layer. These calculations provided estimated average concentrations in the surface layer for a 5-hour period from dawn to 11 UT of 0.3±0.5 ×106 molecules cm-3 for HO, and 3.3±;1.1 ×104 molecules cm-3 for Cl. Noontime concentration estimates were 2.6±0.7 ×106 molecules cm-3 for HO and 6.5±1.4 ×104 molecules cm-3 for Cl. Copyright 1996 by the American Geophysical Union

The structures of Micrococcus lysodeikticus catalase, its ferryl intermediate (compound II) and NADPH complex

The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 Angstrom resolution using data recorded at 110 K and at 1.5 Angstrom resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 Angstrom long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 Angstrom resolution and the catalase complex with NADPH at 1.83 Angstrom resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 Angstrom) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure