Right now they're using separate particles for black and white, with one being positively charged, the other negatively charged, and they apply a charge to the top and bottom of the column the particles are in to cause the two types to move to the top or bottom. When they used 2-color particles, one side had a positive charge, the other a negative charge. I don't know how they'd manipulate particles with more than 2 sides. (I don't think we have that much direct control over quarks yet.
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