Molecular-dynamics simulation of the growth of diamondlike films by energetic carbon-atom beams

The growth of diamondlike films and overlayers by the deposotion of energetic carbon atoms has been investigated by molecular-dynamics simulations. The interatomic many-atom potential suggested by Tersoff is used. The structurel analysis of the grown films shows that there is an energy window between 40 and 70 eV for the deposited atoms where the growth most closely results in dense diamondlike structure. This observation supports earlier experimental suggestions for optimal deposition conditions.Peer reviewe

Computer simulations studies of the catalytic oxidation of carbon monoxide on platinum metals

The steady‐state catalytic oxidation process of carbon monoxide on platinum metal surfaces is studied using two irreversible kinetic computer simulation models: (a) An extended version of the model introduced by Ziff, Gulari, and Barshad (ZGB) with the effects of CO desorption and diffusion as well as finite reaction probability taken into account. The different physical processes, diffusion and desorption are studied independently and their effect on the equilibrium window, i.e., the regime where steady CO2 formation occurs is determined. (b) An interaction model where adatom–adatom nearest‐neighbor (nn) interactions are taken explicitly into account through Boltzmann terms J 1, J 2, and J 3 which are the energies of the CO–CO, O–O, and CO–O interactions, respectively. The phase diagrams in the temperature–CO‐partial pressure (T,p CO− ) plane are determined for different values of the nn interactions. The behavior of the system is dependent on the sign of J 1(=J 2 in the simulations) as well as the sign of the difference J 1−J 3. There is thus a clear analogy with a two‐component equilibrium lattice gas with nn interactions.Peer reviewe

Growth of (110) Diamond using pure Dicarbon

We use a density-functional based tight-binding method to study diamond growth steps by depositing dicarbon species onto a hydrogen-free diamond (110) surface. Subsequent C_2 molecules are deposited on an initially clean surface, in the vicinity of a growing adsorbate cluster, and finally, near vacancies just before completion of a full new monolayer. The preferred growth stages arise from C_2n clusters in near ideal lattice positions forming zigzag chains running along the [-110] direction parallel to the surface. The adsorption energies are consistently exothermic by 8--10 eV per C_2, depending on the size of the cluster. The deposition barriers for these processes are in the range of 0.0--0.6 eV. For deposition sites above C_2n clusters the adsorption energies are smaller by 3 eV, but diffusion to more stable positions is feasible. We also perform simulations of the diffusion of C_2 molecules on the surface in the vicinity of existing adsorbate clusters using an augmented Lagrangian penalty method. We find migration barriers in excess of 3 eV on the clean surface, and 0.6--1.0 eV on top of graphene-like adsorbates. The barrier heights and pathways indicate that the growth from gaseous dicarbons proceeds either by direct adsorption onto clean sites or after migration on top of the existing C_2n chains.Comment: 8 Pages, 7 figure

Energetics and stability of nanostructured amorphous carbon

Monte Carlo simulations, supplemented by ab initio calculations, shed light into the energetics and thermodynamic stability of nanostructured amorphous carbon. The interaction of the embedded nanocrystals with the host amorphous matrix is shown to determine in a large degree the stability and the relative energy differences among carbon phases. Diamonds are stable structures in matrices with sp^3 fraction over 60%. Schwarzites are stable in low-coordinated networks. Other sp^2-bonded structures are metastable.Comment: 11 pages, 7 figure

Dynamic relaxation of the elastic properties of hard carbon films

The effect of enhanced atomic mobility on the growth of hard carbon films was examined. Tetrahedrally bonded amorphous carbon films were deposited by condensing energetic carbon ions using an arc-discharge deposition method. The deposition temperature varied between 50 and 400 °C. The dependence of elastic properties on deposition temperature was examined by determining the frequency-dependent propagation velocity of ultrasonic surface acoustic waves induced by a laser. A remarkable decrease in elastic coefficient was revealed above the deposition temperature of 300 °C and complete relaxation was obtained at 400 °C. This observation was analyzed by using a simple model which was in turn supported by molecular dynamics simulations. The relaxation turns out to be a thermally activated, dynamic process with an activation energy of 0.57 eV. Possible relaxation mechanisms associated with the migration of atoms or defects on a growing surface are discussed.Peer reviewe

Reorganization Energy for Internal Electron Transfer in Multicopper Oxidases.

We have calculated the reorganization energy for the intramolecular electron transfer between the reduced type 1 copper site and the peroxy intermediate of the trinuclear cluster in the multicopper oxidase CueO. The calculations are performed at the combined quantum mechanics and molecular mechanics (QM/MM) level, based on molecular dynamics simulations with tailored potentials for the two copper sites. We obtain a reorganization energy of 91-133 kJ/mol, depending on the theoretical treatment. The two Cu sites contribute by 12 and 22 kJ/mol to this energy, whereas the solvent contribution is 34 kJ/mol. The rest comes from the protein, involving small contributions from many residues. We have also estimated the energy difference between the two electron-transfer states and show that the reduction of the peroxy intermediate is exergonic by 43-87 kJ/mol, depending on the theoretical method. Both the solvent and the protein contribute to this energy difference, especially charged residues close to the two Cu sites. We compare these estimates with energies obtained from QM/MM optimizations and QM calculations in a vacuum and discuss differences between the results obtained at various levels of theory

To retain or remove the syndesmotic screw: a review of literature

Introduction: Syndesmotic positioning screws are frequently placed in unstable ankle fractures. Many facets of adequate placement techniques have been the subject of various studies. Whether or not the syndesmosis screw should be removed prior to weight-bearing is still debated. In this study, the recent literature is reviewed concerning the need for removal of the syndesmotic screw. Materials and methods: A comprehensive literature search was conducted in the electronic databases of the Cochrane Library, Pubmed Medline and EMbase from January 2000 to October 2010. Results: A total of seven studies were identified in the literature. Most studies found no difference in outcome between retained or removed screws. Patients with screws that were broken, or showed loosening, had similar or improved outcome compared to patients with removed screws. Removal of the syndesmotic screws, when deemed necessary, is usually not performed before 8-12 weeks. Conclusion: There is paucity in randomized controlled trials on the absolute need for removal of the syndesmotic screw. However, current literature suggests that it might be reserved for intact screws that cause hardware irritation or reduced range of motion after 4-6 months

Catalytic Cycle of Multicopper Oxidases Studied by Combined Quantum- and Molecular-Mechanical Free-Energy Perturbation Methods

We have used combined quantum mechanical and molecular mechanical free-energy perturbation methods in combination with explicit solvent simulations to study the reaction mechanism of the multicopper oxidases, in particular the regeneration of the reduced state from the native intermediate. For 52 putative states of the trinuclear copper cluster, differing in the oxidation states of the copper ions and the protonation states of water- and O2-derived ligands, we have studied redox potentials, acidity constants, isomerisation reactions, as well as water- and O2 binding reactions. Thereby, we can propose a full reaction mechanism of the multicopper oxidases with atomic detail. We also show that the two copper sites in the protein communicate so that redox potentials and acidity constants of one site are affected by up to 0.2 V or 3 pKa units by a change in the oxidation state of the other site