Figure 1.

(a) An example of a configuration for the ($++$) system, with both knots intertwined. In this configuration, only one prime component(marked in yellow) is identified as “isolated” by our knot identification scheme based on the Minimally Interfering Closure [41]; (b) A small portion of an MD trajectory for the ($++$) system. Yellow shaded regions indicate the portions of the chain occupied by the isolated prime knots, and red and blue lines indicate their first and last bead, respectively. The portion of the chain taken up by the whole composite knot is reported as a gray shaded area. When the knots are intertwined, our algorithm identifies only one isolated knot, which can be seen in the trajectory as a single yellow region surrounded by gray boundaries. Note that the intertwined composite knot can still travel from one side of the chain to the other.