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IBM takes first 3D image of atomic bonds

gizmodo.com

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Re: IBM takes first 3D image of atomic bonds

#51

Post by apotheon »

dsil wrote: post #23
apotheon wrote: post #3

That is fucking awesome. It's depressing to consider the fact that it would probably get downvoted on the science subreddit.

Don't be depressed, it's the top link on science reddit. Though, sadly, the top comment is grammar correction :/

Funny -- last time I checked the science subreddit (just before I unsubscribed), the front page was entirely flooded with ridiculous sensationalism that had little or nothing to do with actual science, while some actually science-focused articles I was watching on the new submissions page were getting downvoted to about -1 or -2 then ignored.

I guess the fact this book comes with pictures probably gives it an edge there.

Re: IBM takes first 3D image of atomic bonds

#52

Post by hughprime »

graphene wrote: post #28
hughprime wrote: post #17

Earlier quoted context omitted.

I'd say it's 3D in the sense that it's a height map rather than a cross section. (We've been able to see cross-sectional images of bonds for some time using transmission electron microscopy, I think). It's not a full three-dimensional structure though, and it'd only work on flattish molecules like this. It should be noted that this sort of resolution has been attainable for some time using scanning tunneling microsco…

about the brightness at the ends - I'm pretty sure that is due to the fact that this is a pi-conjugated system; that is, the pi-bonded electrons can jump around the whole molecule. This, together with the fact that the molecule is finite in size, means that the pi electrons are confined to a rectangle of lower potential energy, and when you solve the quantum mechanics (similarly to the quantum harmonic oscillator) yo…

I'm totally willing to trust the word of someone called "graphene" on this one.

Re: IBM takes first 3D image of atomic bonds

#53

Post by eru »

tel wrote: post #48
tocomment wrote: post #31

Judging by how big of a feat this is to image a molecule, how on earth do we know how things like cellular respiration work? How do we know cells use ATP, etc without being able to watch? (I may make this question a separate post to HN, it's been bothering me for a while.)

Biochemists use easily hundreds of different techniques to elucidate, logically or probabilistically, details about cellular processes. They take serious advantage of techniques like optical properties of solutions and selective targeting of fluorescent tags to visualize effects. Moreover, they tend to abuse the very nanomachine proteins they're trying to study in order to study them further. A simple example (the na…

I second that. My s.o. works in that field. Tiny discoveries mixed with frustration. Still it's fun.

Re: IBM takes first 3D image of atomic bonds

#54

Post by eru »

jwecker wrote: post #45
tocomment wrote: post #31

Judging by how big of a feat this is to image a molecule, how on earth do we know how things like cellular respiration work? How do we know cells use ATP, etc without being able to watch? (I may make this question a separate post to HN, it's been bothering me for a while.)

Not a biologist, but I've been in bio labs and it is _meticulous_ work. Very, very clever processes for detecting molecules as they pass through (or don't pass through) certain organelles, a good dose of math, some inference, and sometimes luck. Not being able to see (and as the toothpick -> truck of floss poster mentioned above, this isn't going to help with biological systems much at this point) does mean there are…

They have to crystalize the proteins to make the xray-technique work.

Re: IBM takes first 3D image of atomic bonds

#55

Post by flipbrad »

speek wrote: post #15
yread wrote: post #8

How is the picture 3D? Also shouldn't we see electrons in pi clouds above the aromatic rings?

Those "clouds" are probability clouds. It means that the electron should be in the vicinity of the cloud at any given time. Also, consider that an electron is 1/1000 the size of a proton.

actually, if you consider that afm is directly detecting charges, I guess we're talking about more than probability here - that picture ought to be a (rough) record of where the charges in that molecule were as the AFM needle passed over the molecule in that 20hr period

Re: IBM takes first 3D image of atomic bonds

#56

Post by flipbrad »

jacquesm wrote: post #6
apotheon wrote: post #3

That is fucking awesome. It's depressing to consider the fact that it would probably get downvoted on the science subreddit.

Second that. Picture of the year as far as I'm concerned. Simply unbelievable. What a time to be alive. So, now that we can 'see' the 3D arrangement in a manner of speaking is there any way we could feed known protein structure in to neural networks by imaging them in quantity and take some of the sting out of protein folding by identifying likely candidate ways to do the folding ? Or is that too big of a leap ?

we've had 3D atomic level detail for molecules - especially horrendously more complex ones than this - for a long, long long time. NMR and X-Ray crystallography in all its guises are the two main candidates here. NMR even gives you that info in real time, and (if you so desire) in more realistic conditions (vital to learn about folding and activity).

Not to piss on a parade, but I don't see this as major breakthrough. It's a technical achievement with an established technology, of primary benefit to material scientists and nanotechnologists, both of whom already have imaging techniques at this level, but lack easy, cheap and instant ones, and face most of their hurdles at the design and synthesis side, not imaging/proof of construct

From a biochemist's point of view, if it was anywhere near real-time, THAT would be awesome.

Re: IBM takes first 3D image of atomic bonds

#57

Post by olavk »

jwecker wrote: post #46
asdlfj2sd33 wrote: post #22

Earlier quoted context omitted.

Color is the wave length of light you can see. Red is one wavelength, blue another, infra red and ultra violet yet another. But you can't see those last two. Molecules have no color because they are smaller then the shortest length wave of light you and I can see. Think about dropping a stone in a quiet pond. Think of the waves that are created. If they bump into a large obstacle they are reflected back. If they hit…

So if I'm a gold atom, and I absorb some photons, a bunch pass through me, and some get reflected - and the photons that are reflected from me over a period of time happen to be average out to something a cone cell in the retina would interpret as gold- couldn't I say that I'm gold-colored? In other words, replacing the billion-atom aggregation with a simple time series? It seems to me it's an argument about semantic…

I think there is some terminology confusion. The image is not a "photo" - it is not a recording of emitted light. Hence the colors used to display the image for us have nothing to do with the color (reflected wavelengths) of the molecules.

Re: IBM takes first 3D image of atomic bonds

#58

Post by ars »

flipbrad wrote: post #55
speek wrote: post #15

Earlier quoted context omitted.

Those "clouds" are probability clouds. It means that the electron should be in the vicinity of the cloud at any given time. Also, consider that an electron is 1/1000 the size of a proton.

actually, if you consider that afm is directly detecting charges, I guess we're talking about more than probability here - that picture ought to be a (rough) record of where the charges in that molecule were as the AFM needle passed over the molecule in that 20hr period

Electrons in an atom don't have a [specific] location. It's not a concept that exists for them. So, yes, it's a probability.

Despite the common image, electrons don't orbit the nucleus like planets around the sun. They sort of exist around the entire thing in all locations at the same time (in 3D, not in a ring, but a shell).

Re: IBM takes first 3D image of atomic bonds

#59

Post by asdlfj2sd33 »

jwecker wrote: post #46
asdlfj2sd33 wrote: post #22

Earlier quoted context omitted.

Color is the wave length of light you can see. Red is one wavelength, blue another, infra red and ultra violet yet another. But you can't see those last two. Molecules have no color because they are smaller then the shortest length wave of light you and I can see. Think about dropping a stone in a quiet pond. Think of the waves that are created. If they bump into a large obstacle they are reflected back. If they hit…

So if I'm a gold atom, and I absorb some photons, a bunch pass through me, and some get reflected - and the photons that are reflected from me over a period of time happen to be average out to something a cone cell in the retina would interpret as gold- couldn't I say that I'm gold-colored? In other words, replacing the billion-atom aggregation with a simple time series? It seems to me it's an argument about semantic…

Ah but protons aren't particles... except some times they are, other times they are a waves. The bottom line is individual atoms don't reflect protons.

Re: IBM takes first 3D image of atomic bonds

#60

Post by graphene »

jwecker wrote: post #46
asdlfj2sd33 wrote: post #22

Earlier quoted context omitted.

Color is the wave length of light you can see. Red is one wavelength, blue another, infra red and ultra violet yet another. But you can't see those last two. Molecules have no color because they are smaller then the shortest length wave of light you and I can see. Think about dropping a stone in a quiet pond. Think of the waves that are created. If they bump into a large obstacle they are reflected back. If they hit…

So if I'm a gold atom, and I absorb some photons, a bunch pass through me, and some get reflected - and the photons that are reflected from me over a period of time happen to be average out to something a cone cell in the retina would interpret as gold- couldn't I say that I'm gold-colored? In other words, replacing the billion-atom aggregation with a simple time series? It seems to me it's an argument about semantic…

that's not the case, the physics in fact is very different for a single atom than for a lump of metal.

A single atom has very specific set of electron energies as a consequence of the electrons being confined to the area around the nucleus. This means that it can only absorb or emit photons with energies corresponding to the spacings between any two energy levels (and the absorption/emission must be accompanied by a jump/fall of an electron between corresponding energy levels. Any type of atom will thus have a secific pattern of absorption/emission peaks, this is incidentally how we can tell the composition of stars and dust clouds in distant galaxies.

For a lump of metal, a good approximation is to consider the electrons as being able to freely roam throughout the entire crystal. As a consequence, when they are excited by an incoming photon (of any energy), they immediately relax back to their original state, emitting the photon again at the same energy. This is why metal films act as mirrors and why metals in general are shiny. As for the goldish color of Gold, that has to do with some relativistic effects which I don't understand (yet ;-) ). I believe the same is true for Copper.

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