Computational modelling of atomic layer etching of chlorinated germanium surfaces by argon.

The atomic layer etching of chlorinated germanium surfaces under argon bombardment was simulated using molecular dynamics with a newly fitted Tersoff potential. The chlorination energy determines the threshold energy for etching and the number of etched atoms in the bombardment phase. Etch rate is determined by bombardment energy.

Coarse master equation from Bayesian analysis of replica molecular dynamics simulations.

We use Bayesian inference to derive the rate coefficients of a coarse master equation from molecular dynamics simulations. Results from multiple short simulation trajectories are used to estimate propagators. A likelihood function constructed as a product of the propagators provides a posterior distribution of the free coefficients in the rate matrix determining the Markovian master equation. Extensions to non-Markovian dynamics are discussed, using the trajectory "paths" as observations. The Markovian approach is illustrated for the filling and emptying transitions of short carbon nanotubes dissolved in water. We show that accurate thermodynamic and kinetic properties, such as free energy surfaces and kinetic rate coefficients, can be computed from coarse master equations obtained through Bayesian inference.

Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes.

Using a coarse-grained molecular dynamics (CMD) approach we study the apparent nonlinear dynamics of water molecules filling or emptying carbon nanotubes as a function of system parameters. Different levels of the pore hydrophobicity give rise to tubes that are empty, water-filled, or fluctuate between these two long-lived metastable states. The corresponding coarse-grained free-energy surfaces and their hysteretic parameter dependence are explored by linking MD to continuum fixed point and bifurcation algorithms. The results are validated through equilibrium MD simulations.

Mechanism of hydrogen-induced crystallization of amorphous silicon.

Hydrogenated amorphous and nanocrystalline silicon films manufactured by plasma deposition techniques are used widely in electronic and optoelectronic devices. The crystalline fraction and grain size of these films determines electronic and optical properties; the nanocrystal nucleation mechanism, which dictates the final film structure, is governed by the interactions between the hydrogen atoms of the plasma and the solid silicon matrix. Fundamental understanding of these interactions is important for optimizing the film structure and properties. Here we report the mechanism of hydrogen-induced crystallization of hydrogenated amorphous silicon films during post-deposition treatment with an H(2) (or D(2)) plasma. Using molecular-dynamics simulations and infrared spectroscopy, we show that crystallization is mediated by the insertion of H atoms into strained Si-Si bonds as the atoms diffuse through the film. This chemically driven mechanism may be operative in other covalently bonded materials, where the presence of hydrogen leads to disorder-to-order transitions.