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Name: Justin
Status: educator
Grade: 9-12
Location: IL
Date: March 2009

Back in 1989, scientists at the IBM Research Center in San Jose, California conducted an interesting activity using atoms. The scientists manipulated 35 atoms of the gas xenon on a nickel substrate, to write the letters, IBM. Why are none of the nickel substrate atoms visible? I have seen other images, since then, with much the same issue: Where are the atoms of the substrate? It always looks smooth! Please help me explain this to my students.

Imaging at atomic scale is quite different than how people see things at our scale. Nanoscale imaging, unlike our eyes, doesn't use light, lenses and detectors, and that means the results may seem counter-intuitive compared to how human eyes work. However, with a little understanding of how nano imaging works, the images produced will make more intuitive sense.

In the famous IBM image, a type of instrument called an STM (scanning tunneling microscope) was used. The principle of operation of an STM is that a very small pointy tip is moved very close to a surface, and when it gets close enough, a small electrical change can be detected. When you move the tip across a surface and measure the height at which the change occurs, you can map out a series of heights associated with different coordinates. Think of it as an atomic topographic map. You can then use software to create an image of the heights and coordinates that "looks like" a photograph.

In this case, the instrument was set up to image the xenon atoms, but not to reach all the way down to the nickel surface between the nickel atoms. The purpose was to emphasize the xenon atoms, not the nickel substrate. That's why they got the image they did. However, they could have imaged the nickel had they so desired. If you Google for STM images, you can see lots of examples of flat planes of atoms being imaged by STM.

Hope this helps,
Burr Zimmerman


The way the "atoms" are imaged is through a process called Atomic Force Microscopy (AFM). As you know, all atoms exhibit a repulsive force (Van der Waal) as though the atom were acting like solid object. AFM uses a technique whereby an atom thin stylus (like in those old style phonographs for vinyl records) that is dragged through the surface of a substrate and the "bumps" produced by individual atoms through their Van der Waal's radius, causes the stylus to deflect. The deflection is measured as a force and converted to an image. The stronger the deflection, the stronger the force, the higher the mound depicted in the computer generated image.

There are two reasons the substrate does not appear to have any bumps (and therefore the atoms in the substrate do not get imaged), is (1) a very uniform patch of the substrate is used so that the bumps are regularly spaced and predictable (usually densely packed silicon crystals), and (2) since the image is essentially computer generated from data, the substrate data -which is very uniform and predictable- can be deleted so that the added information (such as the IBM letters) becomes clearly visible in relief.

Greg (Roberto Gregorius)

Hi Justin,

Once you understand what the Scanning Tunneling Microscope (STM) is doing, the answer becomes more clear. The STM uses a probe that has been sharpened to an incredibly sharp point... a point only one or two atoms at its tip. This probe is "hovered" very accurately over the xenon atoms. In fact, it passes much less than one atom's diameter over the xenon atoms (which, by the way, are much larger than nickel atoms). Using the quantum tunneling effect, the STM (operating via its probe) electrically senses the presence of the Xenon atoms as the probe passes over, and hence a 3D map can be made of their presence (which is in essence what you are seeing). Note that you are not seeing a photo, but only a map of the electric charge.

Whereas the probe passes (and can sense) the xenon atoms at a distance much smaller than an atom's diameter, the probe is too far away from the nickel substrate atoms below, to be able to sense the individual nickel atoms themselves. In a way, it is as if the nickel background is blurred out of focus and all the STM can "see" is a blurred background plane that underlies the xenon atoms.

This is not unlike what happens with a closeup shot using a normal camera. Suppose you were trying to take a shot of an object that was positioned some distance in front of very fine black and white checkerboard pattern. If you focused on the object, it would be very clear, but the background may be so badly out of focus, it might appear as a solid, featureless grey background.

Bob Wilson

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