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.

We implement a computer-assisted approach that, under appropriate conditions, allows the bifurcation analysis of the "coarse" dynamic behavior of microscopic simulators without requiring the explicit derivation of closed macroscopic equations for this behavior. The approach is inspired by the so-called time-stepper based numerical bifurcation theory. We illustrate the approach through the computation of both stable and unstable coarsely invariant states for Kinetic Monte Carlo models of three simple surface reaction schemes. We quantify the linearized stability of these coarsely invariant states, perform pseudo-arclength continuation, detect coarse limit point and coarse Hopf bifurcations and construct two-parameter bifurcation diagrams.

We present a computer-assisted study of ''coarse'' stability/bifurcation calculations for kinetic Monte Carlo simulators using the so-called coarse timestepper approach presented in A. G. Makeev, D. Maroudas, and I. G. Kevrekidis, J. Chem. Phys. 116, 10083 ͑2002͒. Our illustrative example is a model of a heterogeneous catalytic surface reaction with repulsive adsorbate-adsorbate interactions and fast diffusion. Through numerical continuation and stability analysis, we construct one-and two-parameter coarse bifurcation diagrams. We also discuss several computational issues that arise in the process, the most important of which is the ''lifting'' of coarse, macroscopic initial conditions ͑moments of adsorbate distributions͒ to fine, microscopic initial conditions ͑distributions conditioned on these moments͒.

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