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.