

IBM takes first 3D image of atomic bonds - jedliu
http://gizmodo.com/5346964/ibm-takes-first-3d-image-of-atomic-bonds

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ujjwalg
WOW! this is a big breakthrough. I have friends working in my collaborators
group using STM and AFM at UHV (Ultra High Vacuum) and ULT (Ultra Low
Temperatures), and know second hand how difficult/near to impossible it is.

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

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hughprime
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 microscopy, but I'm pretty sure this is a first
for atomic force microscopy. STM doesn't give you a very good image of bonds
-- in fact bonds are generally the thing you _don't_ see, since STM works by
pulling electrons in/out and bonds are stable places where electrons really
don't want to come out of or go into. AFM, on the other hand, shows bonds very
nicely.

You can sorta make out where the aromatic rings are. I'm not sure why it's so
bright at the ends -- any organic chemists out there who can explain that?

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graphene
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) you'll find higher electron density at the
edges of the confining potential.

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

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yan
Are the samples cooled to near zero when scanning like this? As far as I
understand, even slight temperatures cause molecules to move at ridiculous
speeds.

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wwalker3
They said it was a 20-hour scan, at 5K, with the AFM tip 0.5 nanometers from
the pentacene molecule. The molecule itself is 1.4 nm long, so they were only
about 30% of its length away from it in the vertical direction.

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jgamman
great comment on the page: "trivia: molecules have no color" They don't? Then
where does color come from? Why wouldn't gold atoms be golden?

i'm hoping the guy was being sarcastic but...

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asdlfj2sd33
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 a tiny one, like a thin blade of grass sticking out of the water, they
just flow around.

Gold is golden because a whole lot of gold atoms bunched together reflect a
yellowish range of light. Gold the material is gold colored. A single gold
atom does not have color.

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jwecker
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 semantics, not physics.

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asdlfj2sd33
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.

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antaeos
Did you mean photons?

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asdlfj2sd33
Embarrassingly, yes. Obviously I can neither type nor spell well.

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tocomment
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.)

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tel
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 names are removed to make this easier to digest, but if
you're curious it's the action of Glyceraldehyde-3-Phosphate Dehydrogenase in
glycolysis) involves a protein which is known to play a part in the breakdown
of glucose. This protein catalyzes the addition of a "high energy" phosphate
to our compound so we can break it down further while also pulling off a
reactive hydrogen (and adding it to NAD+ to make NADH) so the cell can use
that later (another kind of energy like ATP).

Biochemists, assuming they can already purify the compound and know the
overall reaction, investigated the action of the enzyme by mixing in a highly
reactive fluorescent-tagged molecule that looks similar to the product of the
reaction. This molecule bound permanently to the inside of the enzyme which
was then denatured and sequenced, looking for whatever amino acid showed the
fluorescent tag (cysteine). Then the inserted modified reagents which
contained radioactive hydrogen and phosphate to figure out where exactly those
molecules ended up. In this way they learned where the enzyme added the
phosphate to the product and exactly which hydrogen was removed from the
initial compound to make that NADH.

Biochemistry is a really fascinating story of minute triumphs of discovery.
Unfortunately, like any part of science like that, it means that the day-to-
day life of a biochemist is backbreaking and tedious. Regardless, if you're
interesting, there is a lot of fun stuff to study.

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tel
Oh, and as far as imaging goes, it's simply _amazing_ what has been done with
X-ray crystallography.

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apotheon
That is fucking awesome.

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

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jacquesm
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 ?

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yread
I think there would be major issues getting folded protein to 5K. Plus
proteins "live" in 300K and the oscillations are probably very important for
the function (perhaps even more than a single arbitrary structure you would
get from a picture like this).

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timr
Yes to all of the above. Not to mention that we've long been able to visualize
protein molecular structure using X-rays and NMR. This probably isn't very
useful to anything related to proteins.

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steiger
If that's true, IBM is probably making history (again)

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SapphireSun
Wow this blew me away! Nothing beats visual confirmation from an emotional
perspective ;-)

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TriinT
Where's the URL to the original IBM press release / article? I would rather
read the news from the source, than from those gizmodo subhuman morons any
day...

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sho
_"I would rather read the news from the source, than from those gizmodo
subhuman morons"_

Cut them some slack. At least they're watching/trying. Their article is a news
item here, after all.

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TriinT
Have you read the comments on gizmodo?

They're trying? Trying what? What they usually do is copy-paste from the
source. That does not add much value. Hence, I ask again: where's the URL to
the original press release? I don't want to read such great news from a
website that allows comments from retards who know nothing about Physics...

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sho
I have an easy win for you. Stop reading the comments! They are almost
universally awful.

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TriinT
True. But would it be too far-fetched to claim that the quality of a website /
blog can be indirectly measured by the quality of its comments? A quality blog
should not tolerate certain comments which are more appropriate for YouTube.

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sho
Sigh, when you find the answer to that question, let me know ...

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TriinT
They will never sell _Chanel No. 5_ in gas stations because it would cheapen
it. Likewise, a blog that tolerates retarded trollish comments looks cheap. If
I were one of the IBM scientists who worked on that project, I would hate to
have my work publicized by a blog as distasteful as Gizmodo.

Call me elitist if you will. BTW, my question was rhetorical.

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sho
If you're elitist, it's in a good way. I agree.

