My two cents to this topic:

Find a parameterization of the circle in 3D (the one in u and the other in 
v). Then you can formulate the distance between the circles in the two 
unknows u and v: d[u,v] = ... All you have to do then is to minimize this 
function. You can either do this mathematicaly (partial deriviatives in u 
and v have to be 0) or numerically using something like steepest descent. 
The hardest part is to find the general parameterization in 3D.

- Micha


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