The mixing is done with soft silicone. The silicone is supplied in bulk in a soft raw form. It is then mixed with a hardener which starts a chemical reaction which causes it to set into a firm rubber like material.
During the mixing process other additives, like dyes can be added to give the required colour. Once the mixing finishes, the silicone is still soft, and it can be formed into its final shape. After a few hours it sets hard and stays in its final shape.
I believe this also has something to do with the way our eyes and brain process light. Our eyes only detect 3 different colors, red, blue, and green. Yellow light exists in between true red and true green so both receptors are triggered “half way” and your brain processes this as yellow. If you put yellow paint under a microscope, you actually don’t see yellow and see red specs and green specs, but “zoomed out” you see yellow because your eye receptors are only so small and can’t pic up on the small difference of all those specs and blends them together. So you’re right, the silicone probably just layered the greens and red silicone. But, make enough layers at a small size, your eyes can no longer detect them as separate layers, so it looks yellow.
It’s like folding a sheet of dough and then rolling it out to the original size, each time you do this you halve the thickness of each layer, and double the number of layers. It takes surprisingly few doublings like this for the layers to become atomically thin, and at that point your colorant is thoroughly mixed.
Depending on the rolling technique, each time through the rollers might multiply the number of layers by 10, instead of just doubling it, so you likely only need around a dozen times through the rollers to mix a lump of pigment in so thoroughly you can’t even identify the layers under a microscope.
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