Hacker News Reader

Comment by nathandaly | Hacker News Reader

FYI - This means they're able to image individual atoms, not that they're imagining WITHIN atoms as the title somewhat implies.

That is: atomic resolution, not sub-atomic resolution

View on HN

Pedantic note: they're not really imaging individual atoms directly; it's a composite view of the structure based on averaging thousands of different images of copies of the molecule in different orientations. This is true of other structure determination methods such as crystallography of course. The breakthrough here is that these are exceptionally accurate measurements; when I tried learning EM in the early 2000s it was still mostly just vague blobs.

I remember when those vague blobs were a monumental achievement. It’s very cool to see these kinds of technologies break through and get refined like this.

In terms of either sample prep or data processing, how time consuming is this relative to X-ray crystallography?

Setting aside entirely the enormous benefit of not needing crystals.

I’m a (former) chemist that has only ever had to use X-ray crystallography for small molecules. I’m just trying to get a sense of what the practice of doing this is like?

I do not know what it's like in practice now, but on a purely theoretical basis, if you are trying to solve a completely novel structure with no known homologs, especially if it's something on the scale of a ribosome, direct imaging is always going to be easier than trying to solve the phase problem, both experimentally and computationally.

I don't do much experimentation, but I am pretty sure that you can very easily distinguish individual atoms with electron beam microscopy, and get pretty close using atomic force microscopy. And I am not sure what exactly is the resolving power of synchrotron radiation, but I expect if to be pretty high.

However, the breakthrough here seems being able to do so using a low-energy electron beam. All the methods I quoted above are probably impractical or damaging with biological samples.

With hard xrays you can visualize interatomic densities and lone pairs. I know there are structures down to 0.5Å resolution now but that must have required careful setup. I've seen diffraction out to 0.75Å but I could never collect complete data at that resolution.

I’m imagining a collector plate the size of my dining room table, with a staff of crazy-haired scrawny physicists clambering around some sort of neo-Victorian rube-Goldbergesque X-ray source — like a wine-barrel-sized copper anode and a small nuclear power plant for the arc.

This is not far from the truth, except the detectors are actually relatively small (and very expensive), there's more aluminum foil than the Victorians used, and we have slightly better hair on average. The last time I used one of these facilities, it looked like this (and still does): https://lcls.slac.stanford.edu/sites/lcls.slac.stanford.edu/... Compared to this electron microscopy is downright boring - and a couple of orders of magnitude cheaper to set up.

That's pretty much correct. Single-atom imaging is possible using aberration-corrected scanning TEM, but the beam doses used will typically obliterate anything organic through radiolysis or ionization damage (although there are emerging ways around that using some interesting compressive sensing techniques).

Most "atomic resolution" EM images you see are actually images of columns of atoms, since the imaging mode is transmission, so necessarily the image is summed through the plane of the sample (so atomic resolution is only in the perpendicular plane).

The techniques used in this paper get around the dose issue by taking many images of very many presumably identical proteins (called dose fractionation) at very low dose. Computer algorithms are then used to stitch together a 3D model based on the low-dose individual images. Making it really cold also helps things from breaking down under the beam.

Pedantic note: At this scale, a particle is nothing more than a distribution of the probability of making some kind of measurement. So composites of multiple samples aren't a suboptimal means of imaging atomic structure, they're the only way. To do anything else would be to show only part of the probability field that is the atom.

(Right? I've been going back and forth about this since I saw those "videos" in 2015 of "individual photons". My gut reaction was that those aren't videos, they're simulations that cleverly represent the probability of measuring a photon as the brightness of of the "photon", but since we're measuring inherently probabilistic things maybe that's the only honest way to do it, in which case perhaps we ought to accept them as images.)

Naive question: these images are made at low but finite temperatures, so each atom would fluctuate within its position such that there should be an uncertainty. Is that uncertainty lower than 1 angstrom? Otherwise, how can one talk about atomic resolution if fluctuations are larger?

The uncertainty also comes from averaging many images together. But yes, it's less than 1 Angstrom; the deposited structures (for example https://www.rcsb.org/structure/7A6A) record atomic uncertainties, "B-factors" or "temperature factors" in crystallographer-speak. In the example I pulled out the B-factors are in the low-double digits for the main-chain atoms, and if I'm remembering the math correctly, this will correspond to atomic displacements with a radius around 0.5 Angstrom. (Of course that's just an estimate by the software that performed the model optimization, but my understanding is that this part is relatively straightforward.)

Hmm, but then the b-factor (and therefore also resolution) is dependent on the flexibility of molecule you want to look at? Does that mean that these guys just found a system for which the main chain was rigid enough such that the thermal fluctuations are low enough?

Oh absolutely, they picked a model system that is both very rigid and has extremely high internal symmetry, and I assume they did rotational averaging to use fewer images. But these ideal systems are very useful for determining the limitations of the underlying technology like electron detectors; 15 years ago the best you could do with a molecule like this was around 4 Angstrom resolution.

Ok, that’s fair. But, then the number makes more sense in relative terms than in absolute. Still, absolutely impressive.

This is helpful context. I am not a scientist in any way, shape or form, but this is cool stuff. Appreciate the translation to layman’s terms!

at around 0.7A resolution, you start to be able to see electron density between atoms. Nobody using these methods cares about intranuclear structure, just the electronic structure around the nucleus.

Indeed. For comparison: atoms are about four orders of magnitude larger than atomic nuclei. The size of the former is generally a few tens to low hundreds of picometers (1 pm = 1e-12 m) while the size of the latter is just a few femtometers (1 fm = 1e-15 m).

See, e.g. https://en.wikipedia.org/wiki/Atomic_nucleus for concrete example sizes.

People have used electron diffraction using cryo-em scopes to do sub-angstrom resolution. For example, my colleague Jose Rodridguez published this a few years ago.

https://www.nature.com/articles/s41594-017-0018-0

See also neutron diffraction- it's been used for decades to get fine structure info.

It’s 7 orders for the protium isotope of hydrogen:

https://www.wolframalpha.com/input/?i=diameter+of+hydrogen+a...

One reason hydrogen is so hard to see...

The electron wavefunction scatters primarily off the nucleus potential. The electron cloud acts to screen the potential, but this effect is weak and not easily detected in the scattered wave.

Reply on news.ycombinator.com