On an atomic level, what causes things to stain

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For example if you got permanent marker on a tshirt, what is causing to atoms to stay there?

In: Chemistry
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Stain is a big word.

There are many kinds of stains.

When you spill ketchup on a white shirt. A stain is the red color soaking into the fibers of the cloth, which is absorbent. A powerful detergent that can leach the ketchup partcles out of the cloth may remove it.

When you color something with a felt marker, the stain is a dye that is liquified by a solvent that leaves a solid when the solvent evaporates.

Even permanent markers can be removed from some surfaces with a solvent like pure alcohol.

Some stains are the result of chemical reactions like the white spots from bleach, or peroxide. These are often non removable.