|MadSci Network: Physics|
I've never been good at short answers, so I hope you'll read enough to satisfy your curiosity!
First, let me address the question about why atoms appear so nicely spherical. There are two different ways to think of the electron: particle-like and wave-like (which I'll ignore here to avoid the "funny behavior", as you've aptly described it). Let's consider the particle description. You may be visualizing the atom via the Bohr model (i.e. as solar-system-like), with a large nucleus in the center, and a little particle sitting out a bit from the nucleus. From this mental image, you might expect a big lump (the nucleus) and a little bump (the electron) on any image we obtain. We won't see it that way though because any measurement tool we have is MUCH slower than the movement of the electron. So, just like if we photographed a racetrack and left the camera shutter open for a few hours, all we see is a blur (spherical, in the case of the atom).
Microscopy techniques at this scale rely on some of that "funny behavior". There are three common techniques I'm familiar with, though there may be others (I haven't been keeping up with the bleeding-edge of the field).
Scanning tunneling microscopy (STM) puts an electrical potential (i.e. a voltage) between the microscope probe tip and the object to be imaged. The closer the tip approaches, the more electrons can flow between the tip and the surface (electron flow = electrical current). This 'heigth' of the surface can be measured two ways. In 'constant current' mode, the microscopist selects some current value, and the STM moves the tip closer/farther until the current matches that value. (http://tinyurl.com/9ahpr) In 'constant heigth' mode, we measure the current flowing, and infer the distance from the surface from this. (http://tinyurl.com/2u55j4) The tip gets moved over a grid (i.e. rastered) until there's a distance measurement for all the x and y positions being imaged. This is the key part - the 'image' we see is actually 3D plot of x-probe-position, y-probe-position, z-probe-position|electrical current, not of the surface themselves. It's a subtle but important difference - different surfaces have different conductivities, and since we're actually using current to measure the 'height' this means different atoms might 'stick up' more on the plot (i.e. remember that you're seeing a 3-D chart, not an actual picture!) An example of this can be seen here: http://physics.nist.gov/GenInt/STM/stm.html
Atomic force microscopes (AFM) use a different bit of 'funnyness' to measure height. Here, a probe is moved over the surface to be 'imaged'. Each atom will either attract or repel the tip (and I'm really simplifying how this happens - it could be from contact or a bunch of other things - see http://www.nanoscience.com/education/AFM.html if you're interested.) A laser is reflected off the back of the probe, and as the tip is attracted/repelled, the reflection angle of the laser changes. Again, we aren't so much measuring height as we are measuring attraction/repulsion (though one way to repel the tip is for it's surface i.e. outer electrons to be repelled by the surface's outer electrons aka touching!)
Now, on to moving atoms around. I know of two ways to accomplish this. One is using something referred to as an 'optical tweezer'. Here, light is directed through a microscope objective. Here's where things get tricky, and I'm going to be a little imprecise in my explanation (though if you went the gory details, they're out there!) A photon is capable of generating a pressure (think of those black&white sails in the vacuum bubble that spin when light shines on it!) It's a very small force, but we are talking about very small masses! The key is that the refractive index of the atom/molecule/etc. is higher than its surroundings. The particle ends up 'trapped' in the middle of the light beam, and can be slowly dragged around.
The other method I've heard of for moving atoms is using an AFM to move the atom around. There's a nice summary at: http://focus.aps.org/story/v11/st19 In it I found a wonderful quote to really drive home the relative scales of the AFM probe, the atom, and what's going on between them. "(I)n terms of precision, the task is like using the apex of the Empire State Building to lift a single watermelon out of a watermelon field."
Hope this has been informative!
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