Equilibrium Shape and Size of Supported Heteroepitaxial Nanoislands

We study the equilibrium shape, shape transitions and optimal size of strained heteroepitaxial nanoislands with a two-dimensional atomistic model using simply adjustable interatomic pair potentials. We map out the global phase diagram as a function of substrate-adsorbate misfit and interaction. This phase diagram reveals all the phases corresponding to different well-known growth modes. In particular, for large enough misfits and attractive substrate there is a Stranski-Krastanow regime, where nano-sized islands grow on top of wetting films. We analyze the various terms contributing to the total island energy in detail, and show how the competition between them leads to the optimal shape and size of the islands. Finally, we also develop an analytic interpolation formula for the various contributions to the total energy of strained nanoislands.Comment: 9 pages, 7 figure

Equilibrium shape and dislocation nucleation in strained epitaxial nanoislands

We study numerically the equilibrium shapes, shape transitions and dislocation nucleation of small strained epitaxial islands with a two-dimensional atomistic model, using simple interatomic pair potentials. We first map out the phase diagram for the equilibrium island shapes as a function of island size (up to N = 105 atoms) and lattice misfit with the substrate and show that nanoscopic islands have four generic equilibrium shapes, in contrast with predictions from the continuum theory of elasticity. For increasing substrate-adsorbate attraction, we find islands that form on top of a finite wetting layer as observed in Stranski-Krastanow growth. We also investigate energy barriers and transition paths for transitions between different shapes of the islands and for dislocation nucleation in initially coherent islands. In particular, we find that dislocations nucleate spontaneously at the edges of the adsorbate-substrate interface above a critical size or lattice misfit.Comment: 4 pages, 3 figures, uses wrapfig.sty and epsfig.st

Stress release mechanisms for Cu on Pd(111) in the submonolayer and monolayer regimes

We study the strain relaxation mechanisms of Cu on Pd(111) up to the monolayer regime using two different computational methodologies, basin-hopping global optimization and energy minimization with a repulsive bias potential. Our numerical results are consistent with experimentally observed layer-by-layer growth mode. However, we find that the structure of the Cu layer is not fully pseudomorphic even at low coverages. Instead, the Cu adsorbates forms fcc and hcp stacking domains, separated by partial misfit dislocations. We also estimate the minimum energy path and energy barriers for transitions from the ideal epitaxial state to the fcc-hcp domain pattern.Comment: 4 pages, 4 figure

Ship emissions of SO2 and NO2: DOAS measurements from airborne platforms

A unique methodology to measure gas fluxes of SO2 and NO2 from ships using optical remote sensing is described and demonstrated in a feasibility study. The measurement system is based on Differential Optical Absorption Spectroscopy using reflected skylight from the water surface as light source. A grating spectrometer records spectra around 311 nm and 440 nm, respectively, with the telescope pointed downward at a 30A degrees angle from the horizon. The mass column values of SO2 and NO2 are retrieved from each spectrum and integrated across the plume. A simple geometric approximation is used to calculate the optical path. To obtain the total emission in kg h(-1) the resulting total mass across the plume is multiplied with the apparent wind, i.e. a dilution factor corresponding to the vector between the wind and the ship speed. The system was tested in two feasibility studies in the Baltic Sea and Kattegat, from a CASA-212 airplane in 2008 and in the North Sea outside Rotterdam from a Dauphin helicopter in an EU campaign in 2009. In the Baltic Sea the average SO2 emission out of 22 ships was (54 +/- 13) kg h(-1), and the average NO2 emission was (33 +/- 8) kg h(-1), out of 13 ships. In the North Sea the average SO2 emission out of 21 ships was (42 +/- 11) kg h(-1), NO2 was not measured here. The detection limit of the system made it possible to detect SO2 in the ship plumes in 60% of the measurements when the described method was used. A comparison exercise was carried out by conducting airborne optical measurements on a passenger ferry in parallel with onboard measurements. The comparison shows agreement of (-30 +/- 14)% and (-41 +/- 11)%, respectively, for two days, with equal measurement precision of about 20%. This gives an idea of the measurement uncertainty caused by errors in the simple geometric approximation for the optical light path neglecting scattering of the light in ocean waves and direct and multiple scattering in the exhaust plume under various conditions. A tentative error budget indicates uncertainties within 30-45% but for a reliable error analysis the optical light path needs to be modelled. A ship emission model, FMI-STEAM, has been compared to the optical measurements showing an 18% overestimation and a correlation coefficient (R-2) of 0.6. It is shown that a combination of the optical method with modelled power consumption can estimate the sulphur fuel content within 40%, which would be sufficient to detect the difference between ships running at 1% and at 0.1%, limits applicable within the IMO regulated areas

First principles structures and circular dichroism spectra for the close-packed and the 7/2 motif of collagen

The recently proposed close-packed motif for collagen is investigated using first principles semi-empirical wave function theory and Kohn-Sham density functional theory. Under these refinements the close-packed motif is shown to be stable. For the case of the 7/2 motif a similar stability exists. The electronic circular dichroism of the close-packed model has a significant negative bias and a large signal. An interesting feature of the close-packed structure is the existence of a central channel. Simulations show that, if hydrogen atoms are placed in the cavity, a chain of molecular hydrogens is formed suggesting a possible biological function for molecular hydrogen.Comment: 12 pages, 3 figures; 3(PPG)_6 xyz file attached; v2: minor modification

Effects of mannose, fructose, and fucose on the structure, stability, and hydration of lysozyme in aqueous solution

The bio-protective properties of monosaccharaides, namely mannose, fructose and fucose, on the stability and dynamical properties of the NMR determined hen egg-white lysozyme structure have been investigated by means of molecular dynamics simulations at room temperature in aqueous solution and in 7 and 13 wt % concentrations of the three sugars. Results are discussed in the framework of the bio-protective phenomena. The three sugars show similar bio-protective behaviours at room temperature (300 K) in the concentration range studied as shown by the small RMSDs of the resulting MD structures from that of starting NMR structure. The effects of sugars on protein conformation are found to be relatively strong in that the conformation of lysozyme is stable after an initial 9 ns equilibration for fucose and mannose and 12 ns equilibration for fructose, respectively, at high concentrations. For mannose the final RMSD is significantly smaller than that of fucose and fructose at the higher concentration, while at the lower concentration the RMSD are essentially the same. The radial distribution function of the water and sugars around lysozyme was used to monito

Two Approaches to Dislocation Nucleation in the Supported Heteroepitaxial Equilibrium Islanding Phenomenon

We study the dislocation formation in 2D nanoscopic islands with two methods, the Molecular Static method and the Phase Field Crystal method. It is found that both methods indicate the same qualitative stages of the nucleation process. The dislocations nucleate at the film-substrate contact point and the energy decreases monotonously when the dislocations are farther away from the island-wetting film contact points than the distance of the highest energy barrier.Comment: 4 page