Fantastic tutorial on Video Copilot that shows some of the possibilities available using After Effects. The illusion of moving through strata could be an excellent illustrative technique to show vertical relationships.

The 3ds Max software, released by Autodesk, allows users to model, animate, and render objects and systems with a large degree of freedom and accuracy. The Particle Flow program is a simulation system built into 3ds Max. It allows for non-linear events to drive the parameters of the system. Complex phenomena such as water, air, and photon-scale light behavior can all be modeled in the particle flow system.

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