Spiral patterns in the full zipper graph (another post on the Chemical concrete machine)

A step for making something analogous to the Holliday junction, such that it is related to the Chemical concrete machine minimal formalism, is to make a full zipper. Let’s play with it.

I shall use two ingredients, which function only by using the graphic beta move, so I shall NOT use the FAN-IN move.

fullzipper_1

  • zippers, this time written with the conventions of the Chemical concrete machine minimal formalism.

fullzipper_2

If we put them together then we obtain graphs like this: (ignore for the moment the red and green curved  arrows, suppose they are not there)

fullzipper_3

Now, if we want the numbering 1-1′ 2-2′ 3-3′  to make sense, we may add arrows, the green and red ones. But mind you, we could also add graphs with one input and one output instead of each green or red arrow.  As usual, the colours are just a visual help, they mean nothing in the formalism.

Is just a play, but for the moment, since it’s holiday season, I like to think about the green and red arrows (in fact about their replacements by graphs with one input and one output) as being the letters A, C, G, T. Of course, it might mean nothing, let’s see, it’s just a vague hypothesis.

Left for play: draw a Holliday junction.

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