You can't. At least, you can't see an atom with the naked eye, and not even with a regular microscope. Since atoms are too small to see without the most advanced technology, scientists created a special type of microscope to detect and depict them.
In 1981, the scanning tunneling microscope (STM) was invented. An STM is made up of instruments that collect information about specific atoms, and then relay that information to a computer, which controls the system and creates a rendering of the atomic pattern. The STM works by running an electrified scanner tip over the sample area (picture the arm on a record player running over a record). When an atom is touched, the flow of the electrons between the atom and the STM tip changes, giving the STM computer the location of that atom. As the STM tip scans the sample area, it sends all the plotting data about the atoms to the computer. The computer then uses this information to create a rendering [source: TU Wien].
STM, as well as new variations of electron microscopes, can also manipulate atoms, which is extremely important to the burgeoning field of nanotechnology. Being able to depict and manipulate atoms at an increasingly closer range will help scientists learn more about how the atom and its various parts can be used in scientific research. The STM is so important that in 1986, its inventors, Gerd Binnig and Heinrich Rohrer, received the Nobel Prize for physics.
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