There's a couple different things going on in From Dust, but I think the basic thing you're looking for is the [Marching Polyhedrons][1] algorithm. It's used to generate a 'shell mesh' over a point cloud. You can animate the point cloud however you want. If you want flowing liquid, you'd use something like the [navier-stokes][2] equations for simulating fluids.
This stuff is all pretty math heavy theory, but it's good to know the basics. To implement it you'd want to go for one of the papers that SIGGRAPH puts out each year on realtime fluids.
[1]: http://en.wikipedia.org/wiki/Marching_tetrahedrons
[2]: http://en.wikipedia.org/wiki/Navier%E2%80%93Stokes_equations
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