Is there a mathematical theory of physical knots?
Solution 1:
I don't know the explicit content of this course at MIT, but it may be of interest:
http://math.mit.edu/~ormsby/knots.html
And here is a link to a piece about Fields Medal winner Vaughan Jones describing his work on knots. It's a bit removed from your practical questions, but clearly reflects a link between physics and knots
http://blogs.vanderbilt.edu/research/2011/04/beyond-knot-theory/
Solution 2:
http://en.wikipedia.org/wiki/Physical_knot_theory
http://en.wikipedia.org/wiki/Knot_energy
I suspect that the theory is not well-developed as it applies to the examples in the posted question.