Re NanoEnthusiast’s suggestion: (I’m sure this isn’t news to the Sandpit people, but for others reading the comments:) Covalent structures are not generally delicate enough to require such intricate techniques. Here’s a quick analogy. A blind person might have trouble repairing a watch. But a blind person could solve a Rubik’s Cube with braille faces instead of colors–could easily read the faces without rotating the cube accidentally.
A major reason we can’t “see” nanoscale mechanical structures is because photons are too big. Then, in the absence of photons, we have to use interactions and phenomena we’re not used to, and have to work hard to figure out what the signals mean. Also, our tools are vastly bigger than what they’re measuring, and thus hard to use. So it is not at all simple to “see” the nanoscale. But there are a lot of things of interest that we can probe without disturbing.
Here’s a more detailed analogy. It’s not a direct physical analogy with a scanning probe microscope, but it’s pretty close. Suppose you were trying to read Braille with a toothpick. If you had good muscle control and spatial sense, you could do it pretty straightforwardly. Sure, you *could* poke the toothpick through the paper, but you wouldn’t normally worry about that. That’s the physical limit–a toothpick can poke through paper–and that’s how much you have to worry about it in theory. So what is it that makes SPM hard to do?
Take a telephone pole and hang it sideways from milspec bungee cords so it looks like a battering ram. Put a toothpick sticking out of one end. Position a Braille book next to the toothpick*. Stand at the other end. Now try to read the Braille. You could still do it… the pole transmits force well and requires very little force to move, so it should be sufficiently sensitive… if you had the patience to move the telephone pole *very* slowly and delicately, and a good enough kinesthetic sense to track the force feedback. With a mechanical system to do the scanning and measuring, rather than human muscles and nerves, you should be able to read Braille just fine, albeit slowly… as long as the page didn’t move, and the bungee cords didn’t slowly stretch, etc. It’d certainly be a non-trivial engineering problem.
Although it’s difficult to scan Braille with a telephone pole, the size and inconvenience of the pole (or scanning probe microscope) don’t have any direct connection to the size of things you can measure. And the delicacy of certain nanoscale or quantum phenomena doesn’t have any direct connection to the strength of covalent structures.
Just because the telephone pole *looks* like a battering ram, doesn’t mean that the weight of the pole will drive the toothpick through the paper. Just because the system is cumbersome, doesn’t mean that it’s running into deep physical limits. Just because careless operation can easily destroy the book, doesn’t mean that paper is too delicate to be touched by toothpicks.
And although there are probably experimenters right now doing SPM experiments that do run up against deep physical limits, there are lots of other experimenters making SPM images of atoms in crystals without coming close to knocking the atoms loose.
* In fact, you have to bring the pole to the book rather than placing the book next to a pole hanging still, and you don’t know exactly where the book is. So you have to move the gantry crane that the pole is hanging from… while continually sensing whether it’s touching the book yet. Not easy–but SPMs actually do this. And another thing–the “toothpick” is actually more like a golf ball or thimble–much bigger than the Braille dots, but it has a lowest point that can be used to scan them.
I should mention thermal noise. Oh yes, the book is vibrating… but it’s usually vibrating less than the width of a Braille dot, and even if it weren’t, you could sense the *average* position of the dot by looking at the *average* force between the dot and the toothpick. Now, if you had a non-covalent system like small molecules resting on a surface, the atoms might actually move around, and the microscope could be too slow to watch them, and only see them statistically. A large molecule like a buckytube won’t move by itself at room temperature, but can be pushed–this is actually quite useful.
I hope this explanation isn’t too long-winded for this blog, and didn’t make too many simplifications and analogies that will annoy the real scientists. Perhaps I should have just skipped to the summary: Scanning probe microscopes scanning covalent solids are limited a lot more by practical (e.g. mechanical) problems than by foundational physical limits or quantum phenomena.