[HN Gopher] Atomic resolution video of salt crystals forming in ...
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Atomic resolution video of salt crystals forming in real time
Author : rbanffy
Score : 330 points
Date : 2021-01-22 18:28 UTC (4 hours ago)
(HTM) web link (www.u-tokyo.ac.jp)
(TXT) w3m dump (www.u-tokyo.ac.jp)
| zaroth wrote:
| Truly mind blowing being able to actually see the atoms align in
| an instant and the crystal structure just pop into existence.
|
| Hard to believe it's not a computer model. I mean, I guess
| underneath there must be a hell of a lot of signal processing
| going on to render that video, but atomic-scale video is wild.
|
| Funny that it looks kinda like MPEGS online circa 1990s.
| mywittyname wrote:
| I also love how you can see the probabilistic nature of
| electron orbitals in action. The crystal fades in and out of
| existence during the early stages of nucleation. And even after
| the structure is established, the boundaries continue to be
| "fuzzy."
|
| Even the movement of the crystal looks like a wave, but I don't
| know if that's because matter moves as a wave at the atomic
| level or if that's just an artifact from the camera.
| jng wrote:
| I would think that the coming in and out of view at the
| beginning is more related to the crystal moving around and
| falling "in and out of focus" (whatever that means for this
| type of camera). I'd love to watch quantum probability wave
| fluctuations, but I think we're still pretty far from probing
| that.
| jtaillon wrote:
| In this case, "in and out of focus" is actually variations
| in the amplitude of the probability function for the
| electron density projected onto a single plane (to a first
| approximation). Sometimes the wave functions of all the
| electrons interfere constructively, so you see a bright
| spot, and sometimes deconstructively, so you see dark.
| Depending on the orientation of things, this results in the
| images of "atoms" that you see in the picture. As the
| crystal changes shape and size, the interference patterns
| change, which partially explains why it disappears and
| reappears a few times. There's a bit more going on than
| that, but the physics of what's happening in a TEM image is
| really neat.
| jng wrote:
| Wow, mind blown. Thanks for correcting me. Amazing to
| learn that the wave function is so directly sampled by
| TEM that the image we get shows Moire patterns caused by
| its phase :)
| Osmium wrote:
| > I don't know if that's because matter moves as a wave at
| the atomic level or if that's just an artifact from the
| camera.
|
| Artifact of the imaging, note the time scale of the movie,
| it's much longer than any quantum oscillation. Each
| individual image of the movie is taken eons apart from the
| perspective of the crystal.
| magicalhippo wrote:
| > Each individual image of the movie is taken eons apart
| from the perspective of the crystal.
|
| Given the timescales of atomic reactions, which IIRC is
| typically measured in nano- or picoseconds, this video is
| more like watching galaxies form I suppose.
| kvakkefly wrote:
| You may also like my paper " Direct Atomic Simulations of Facet
| Formation and Equilibrium Shapes of SiC Nanoparticles"
|
| Not as cool as experiment of course
|
| https://pubs.acs.org/doi/full/10.1021/acs.cgd.9b00612
| blix wrote:
| This is a neat paper. Cool to see kinetic phenomena make it's
| way into MD. How many GPU-hours did you need to get those 500ns
| simulations?
|
| You should throw up some videos of these somewhere, if you have
| the time.
| peter_d_sherman wrote:
| _Star Trek 's Replicator -- version 0.000001..._ <g>
| vhold wrote:
| There are video files here :
| https://pubs.acs.org/doi/10.1021/jacs.0c12100?goto=supportin...
| fantod wrote:
| This is super cool but who's idea was it to feature the video as
| a pretty small gif on the side of the page?
| codezero wrote:
| literally every grad student in science fields - they don't
| care about video compression or download quality - and gifs are
| fast and easy to make and simple to grok and come out with
| straightforward and predictable fidelity.
| jasondclinton wrote:
| Non-physicist question: why does the block of the forming crystal
| move as a whole back and forth? Is this Brownian motion in
| action?
| magicalhippo wrote:
| The containing structure (the carbon nanohorn as they call it),
| is vibrating. So I'm guessing it's getting kicked around when
| it touches the walls, so to speak.
| hindsightbias wrote:
| Guessing the crystals are probably connected in some lattice so
| won't move independently. The expansion horizontally is gated
| by the walls so it gets bounced around until it moves to a
| wider section. There seems to be some ratio of horizontal vs
| vertical growth.
| jagraff wrote:
| This is incredibly cool:
|
| > Two novel techniques, atomic-resolution real-time video and
| conical carbon nanotube confinement, allow researchers to view
| never-before-seen details about crystal formation. The
| observations confirm theoretical predictions about how salt
| crystals form and could inform general theories about the way in
| which crystal formation produces different ordered structures
| from an otherwise disordered chemical mixture.
|
| > To hold samples in place, we use atom-thick carbon nanohorns,
| one of our previous inventions. With the stunning videos
| Sakakibara captured, we immediately noticed the opportunity to
| study the structural and statistical aspects of crystal
| nucleation in unprecedented detail.
|
| Creating shaped nucleation sites using carbon nanotubes
| (nanohorns?) sounds like a fascinating technology. I don't have
| access to the paper unfortunately - I'm curious what other types
| of crystals could theoretically be grown with this technology.
| The authors mention graphite - what about silicon? Could it be
| used to grow more regular crystals for use in electronics? With
| fewer defects, I'd imagine we could reduce the failure rate in
| manufacturing.
| grishka wrote:
| > I don't have access to the paper unfortunately
|
| The website you're looking for starts with sci and ends with
| hub.
| sebmellen wrote:
| Not up there yet. Probably needs a few weeks, unless a HN
| reader is so kind as to add it: https://sci-
| hub.se/10.1021/jacs.0c12100.
| Ericson2314 wrote:
| Are you angling for some scintillating chub?
| [deleted]
| codercotton wrote:
| Super cool, where's my replicator?
| curtainsforus wrote:
| Just build your own
| [deleted]
| thepace wrote:
| Every time I see these kinds of video, whether that is of protein
| translation, kinesin walking on microtubule, or birth and death
| of a galaxy, I get this feeling that Panpsychism is closer to
| truth that it gets credit for. Any constraints we put in the
| defining consciousness and life seems to be just some arbitrary
| constraint put there for our own convenience.
| wahern wrote:
| Panpsychism, pantheism, etc, are enticing because humans are
| predisposed to see patterns, structure, reason, and
| intelligence; to anthropomorphize nature. Characterizing as
| "arbitrary" our admittedly feeble and flawed attempts at
| distinguishing the human mind is an easy way to placate that
| underlying, intrinsic desire.
|
| Of course, maybe it is true! (That felt good to say :)
| TeMPOraL wrote:
| Isn't panpsychism a kind of reverse materialism? Both seem to
| correctly recognize that terms we create are just lines we draw
| on our map through the terrain of reality, which we rank by
| their usefulness, by how close they seem to be "carving nature
| at its joints". Based on my brief skimming, panpsychism seems
| to say the terrain is all mysterious and wonderful, whereas
| materialism says it's all just mundane.
|
| Or am I completely mis-skimming the Wikipedia entry on
| panpsychism?
| perfmode wrote:
| my question to you: do you consider yourself to be mysterious
| or just mundane? what is your experience of your own Being-
| ness?
| TeMPOraL wrote:
| A good question, something I'll have to think about.
|
| The immediate if indirect answer I can give you: I stopped
| feeling this sense of wonder, mystery, greater purpose of
| reality, somewhen during my university years. I only ever
| experience these feelings when consuming works of fiction.
| lewispollard wrote:
| I think you'd enjoy the work of Bernardo Kastrup, who is a
| proponent of idealism, while also arguing against
| panpsychism, for basically the reasons you just stated - ie,
| there is a reality made of parts, and those parts are x,
| where x is 'matter', 'mind', 'consciousness',
| 'electromagnetism' and so on. But the trouble then is that
| you can only describe the constituent parts in terms of those
| parts. For example, subatomic particles have properties like
| spin and charge, but that's the only way you can describe
| them - in relation to one another - without having to go a
| level 'deeper' if it were possible to describe them in
| further parts (which would only be describable in terms of
| those parts, and so on).
| csomar wrote:
| > Any constraints we put in the defining consciousness and life
| seems to be just some arbitrary constraint put there for our
| own convenience.
|
| The definition of consciousness is very much tied to how humans
| (or some scientists) perceive consciousness. I'm pretty sure my
| dog is conscious of itself and its surrounding. It just happens
| to have a less sophisticated consciousness than the one I have.
| Some animals might have a pretty high consciousness but they
| fail to communicate it to the humans.
| kharak wrote:
| I can't see this connection at all. Could someone who thinks or
| feels this way elaborate?
|
| Does this feeling arise because those atoms move? Or is it the
| self-assembling behavior? Is this the same feeling some people
| have when they see a door suddenly close due to the wind, as if
| some spirit is responsible? I remember feeling like this as a
| kid. But getting older, I realized that this feeling of agency
| behind everything is unfounded. And the feeling faded away.
| jes wrote:
| I am an Alan Watts fan. I think he would agree with you.
| djedr wrote:
| He would definitely dig that. Curiously, I was drawn to this
| thread because I was just listening to him today, talking
| about crystals and the nature of reality. He would go thru so
| many topics in such detail and clarity, it's incredible.
| jng wrote:
| I love Alan Watts too. In any case, I need to insert the
| necessary reference to recently passed John Conway's Free
| Will Theorem. I recommend every one to watch his 6-lecture
| long presentation on this, available on YouTube and
| underappreciated given the number of views, where he
| captivatingly describes his proof that, if we have free will,
| so do elementary particles. This is a purely mathematics- and
| physics-based proof which I understand is fully accepted by
| the scientific community, and while it, of course, does not
| provide an explanation of the underlying cause, it provides
| the best possible description obtained by scientific
| methodology so far.
|
| I like to think that, somehow, Alan Watts and John Conway
| were digging the same tunnel, just starting from the two
| endpoints, and bound to meet at some point in the future. We
| just need a few more diggers of that stature (tall order, I
| know).
| [deleted]
| jcims wrote:
| I'm curious how they managed to make it happen so slowly. If that
| crystal had grown to 100 molecules in 10 seconds it would take
| roughly the age of the universe to form a grain of table salt.
| jacquesm wrote:
| The growth rate is proportional to the surface area.
| goalieca wrote:
| They confined the reaction to a tiny horn.
| dragontamer wrote:
| > "Salt is just our first model substance to probe the
| fundamentals of nucleation events," said University Professor
| Eiichi Nakamura. "Salt only crystallizes one way. But other
| molecules, such as carbon, can crystallize in multiple ways,
| leading to graphite or diamond. This is called polymorphism and
| no one has seen the early stages of the nucleation that leads to
| it. I hope our study provides the first step in understanding the
| mechanism of polymorphism."
|
| I'm amused that Chemists / Physicists also have the word
| "Polymorphism" and that it means something completely different
| from the programming term.
| flobosg wrote:
| It's also a term used in biology:
| https://en.wikipedia.org/wiki/Polymorphism#Biology
| skulk wrote:
| My second confrontation with the term "polymorph" was a Java
| tutorial, the first was Larn
| (https://larn.fandom.com/wiki/Spells)
| MereInterest wrote:
| In some ways, they are sort of related. In chemistry, you have
| different representations (diamond/graphite) of the same
| underlying thing (carbon). In programming, you have different
| representations (PointXY/PointRTheta) of the the same
| underlying concept (Point2D).
| jxramos wrote:
| right, the roots of the word make it applicable to lots of
| stuff, poly or many, morph or structure/form.
| adrianmonk wrote:
| Arguably it's the strategy pattern. Graphite and Diamond
| are subclasses of CrystalizationStrategy.
| soheil wrote:
| This looks like how microscopic proteins and bacteria move in the
| body. I wonder how much of their motion is caused by the atomic
| level forces that form a lattice structure similar to that of
| salt crystals.
| rightbyte wrote:
| The "tube"/horn is vibrating. I would make that connection from
| the gif. The scale difference is quite big.
| adrianmonk wrote:
| Amazing achievement! Not only the world's first video of this
| type, but I imagine also the world's smallest salt shaker.
| [deleted]
| frongpik wrote:
| Another interesting experiment is the effect of strong magnetic
| fields on crystals: when the field is turned off, is there
| something left in the crystal, e.g. a certain motion pattern of
| crystal nodes?
| jerzyt wrote:
| What is absolutely mind blowing to me is that when I was in
| college, in my crystallography class, we were inferring the
| crystal structure through the X-ray diffraction. Now we can
| observe it directly. I took the crystallography class in late
| 70s. I doubt that anyone had expected so much progress.
| 6nf wrote:
| In the same vein, I'm blown away what we can do with xray
| crystallography these days! Structures of proteins with
| hundreds of atoms can somehow be deduced from some tiny light
| spots in a kaleidoscope picture? Magical.
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