MacResearch

Results of molecular dynamics calculations performed with OpenMacGrid recently appeared in an article in the Journal of Chemical Physics [J. Chem. Phys. 128, 194715 (2008); DOI:10.1063/1.2920488]. The study included results from classical molecular dynamics, which were performed on OpenMacGrid, and the first ever full-dimensional quantum dynamics calculations for a stepped-surface reaction. The latter are very expensive, and were performed on a massively-parallel supercomputer.

Stepped surfaces, and other ‘rough’ surfaces, play an important role in heterogeneous catalysis, where they generally exhibit higher reactivity than corresponding flat surfaces. This is thought to result from a lowering of the potential energy barrier to reaction in the region of the rough features. But the OpenMacGrid study shows that the steps can introduce a secondary reaction mechanism, which further enhances reaction, by trapping molecules near the surface, allowing them more time to migrate to a reactive site.

The classical study was performed on OpenMacGrid because classical trajectories can be calculated independently of one another, making the calculations trivial to parallelize, and requiring no communication between compute nodes. Quantum mechanics is inherently delocalized, meaning that considerable communication is required, and a supercomputer architecture is more appropriate.

The study looked at reaction of hydrogen gas molecules impacting a platinum surface. The hydrogen molecules can be ‘dissociated’, splitting into individual atoms, and sticking to the surface. Although a lowering of the barrier at the platinum steps certainly increased reactivity, it was found that a mechanism involving molecular trapping further enhanced reaction at low energies. This was found to be the case in both the classical and quantum calculations, though the specific details varied somewhat.

Analysis of results was carried out on desktop Macs, and involved the use of customized visualization software written with Cocoa and the Visualization Toolkit. (Tutorials on using VTK with Cocoa are available on MacResearch.) Movies were generated showing the evolution of the classical and quantum gases, which were useful for identifying the nature of the molecular trapping mechanism, and quantum interference effects.