This are voronoi cells from the particle positions. The dark cells are the defects. The first picture is the template layer and the second picture is the layer on top of it. The the third one is the forth layer. The interesting thing is that there is an annealing in the second layer.
Computational geometry is quite powerful.
Here is something that I help a biologist with. We triangulate the 'skeleton' inside the cells. Then by observing the 'deformation' of those triangles under the flow, we can calculate the local stress tensors under the shear. This project started by a REU student, Evan Holhfield, in summer 1999. I was his supervisor.