Dip Pen Nanolithography, how it's done
The method is actually pretty simple.  It works just like a printer, moving back and forth over a surface.  Only the AFM tip would write on the x and y axes of a coordinate plane.  Literally, the tip would graph what is programmed to be written.


While manipulating the AFM tip across a plane, the ink is transported onto the substrate through a water meniscus.  The ink molecules, or atoms, jump from the tip to the substrate because of a strong polar bond.
http://www.zyvex.com/nanotech/feynman.html
Richard Feynman's speech written at the nano scale.
http://www.chem.nwu.edu/~mkngrp/dippen.html
Diagram of the writing process.
http://www.chem.nwu.edu/~mkngrp/dippen.html
A) Ultra-high resolution pattern of mercaptohexadecanoic acid (the ink) on atomically-flat gold surface. B) DPN generated nanostructure with two aligned alkanethiol patterns. C) Richard Feynmann's historic speech written using the DPN nanoplotter.
More information can be found at:

Nano Ink, Inc.
Chad Mirkin's DPN Group
LEFT: see a DPN movie at nanoink.net
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