Home-Built Scanning Tunneling Microscope (2015) | Hacker News Reader

Home-Built Scanning Tunneling Microscope (2015)

dberard.com

361 points_Microft79 comments

His day-job is pretty mind-blowing, too. He basically works on combing DNA, by squashing it "into nanogrooves [that] are less than 50 nm"

https://dberard.com/research/

edit: added description of his work

This project is great.

Last semester at university lab, our group tried to rebuild it in our lab.

Through our spectacular fail, we learned how amazing this project actually is. It is harder than it seems.

One can learn very much about piezo electronics, especially about OPamp circuits. And do not underrate the damping!

And the amplification circuitry, that's not trivial. I was actually surprised he got away with having the wiring out in the open without shielding it for EMI.

In the section for "Electronics" is this line "I place a metal can over the STM during scanning to shield the tip and preamp. Without the shield, the images produced by the STM are dominated by 60 Hz noise pickup."

Ah! I totally missed that, thank you. I thought the pictures were of the scanner in operation, and that detail really confused me.

I worked with a simple STM in a lab exercise. At the beginning, we created a new, clean tip. Guess how we did that?...

We cut a piece of ordinary steel wire diagonally with an ordinary wire cutter. Somehow we did it right - the first one worked. It was all somewhat fiddly and sometimes the image was noisy. But we did get images of atoms.

I haven't thought about tips in a while... definitely part of the "magic" of STM. Cutting a wire under tension sounds like it was a pretty common technique, it's the one my lab was using too.

If the imaging just wasn't happening, it was common to goose the bias voltage (10x) for a split second in hopes of perturbing the tip enough to get things to go.

This reminded me of a Thunderf00t video where he created tiny jets for ammonia. I expected it would be some expensive procedure, but he just heated up some glass, stretched it and cracked it. Not every one worked, but it was surprising how mundane some super precise tooling can be

If your process can be "make a tonne of low-precision instances then screen for accuracy" you can get surprisingly good results in general, as long as the accuracy of each instance is relatively uncorrelated. It's a really handy pattern to have in your back pocket.

I think I'm going to build this with my kids. What better way to show them atoms than to actually make them build a microscope that shows you the things directly?

There's also this recent DIY project: laser confocal microscope which also seems to be a fun build: http://www.gaudi.ch/GaudiLabs/?page_id=652

Laser confocal microscope seems to be a little more relatable/less abstract (um vs nanometer scale).

This is a wonderful idea. Children (and adults) learn best by doing. There's such a big difference between watching some tv show and making an actual experiment to see structures invisible to the naked eye. I know I would have been psyched to see atoms as a kid.

I'm sure its a cool project.

But its not showing things directly, is it? Its interpreting a frequency and converting that to an image. Is it really that different to a music visualiser?

Directly as in: you do it yourself, without going through a bunch of intermediaries who will dazzle you with their pretty pictures, you yourself are the one observing the results.

Of course a STM does not work with visible light so it's pretty damn obvious that any measurements will use some other mechanism, and will have to have their measurements converted into an image that we can see. But that does not mean we are not observing. As opposed to reading about someone else's observations.

I take it you also believe that quasars have not been observed and ditto for the dark side of the moon?

I mean, what is your brain doing if not that?

You don't think there's a difference between what you see with your naked eye, and what is visualised for you by sensors and software?

Sure, but digital cameras are still useful.

There are an incredible number of recurrent top-down connections in your vision processing areas. You do not really see what's there in any meaningful way. What you see is heavily conditioned on what other modules of your brain "expect" to see.

Consider foveated vision. The idea that you can actually see what is going on on your desk all at the same time is an illusion.

do you think your eye is not a sensor ?

Of course your eye is a sensor. As are all your senses. The difference is that the input it receives is unmediated by external sensors and software. Visualising atoms or DNA is fine, but it is an inferior source of information. By a long way.

Imagine you were born deaf and couldn't hear music. But that someone showed you a music visualiser.

Do you think if you were watching the output of that visualiser you would now know the music in some meaningful way?

Would it be possible for you to try at least to contribute to the discussion? This out of hand dismissal seems to be a bit of an issue for you, maybe try harder?

https://news.ycombinator.com/item?id=26743591

How is it inferior? We can't see in for e.g. the IR spectrum. But we can turn an IR image into a false-colour image that our eye and brain can make great use of. Using your eyes to directly see in IR will inherently be inferior to processing the results from a sensor into a form that we can see.

You seem really hung up on some pedantry about "see" and "seeing". Why? This may seem like some kind of strong criticism to you, but it just seems as though you are unaware of these technologies and haven't really thought through what constitutes a measurement or observation.

> But its not showing things directly, is it?

I don't understand the downvotes. That's an honest fundamental question.

It's not "showing things directly" because it can't. The limit of what you can see with light is proportional to the wavelength of the light (this is called the diffraction limit). For visible light and lens-based optics that's around 1/2 micron.

The distance between the atoms in that graphite is ~3 angstroms, that about 2000 times smaller than the diffraction limit for visible light.

You CAN get atomic resolution with a transmission electron microscope. Instead of light it uses electrons and has a far finer diffraction limit that visible light. Instead of lenses it uses electrostatic deflection.

> I don't understand the downvotes.

Because the comment is factually wrong. Because it tries to argue something in bad faith.

> That's an honest fundamental question.

But it wasn't a question, it was a statement, and a faulty one at that.

Best case interpretation would require substituting 'current' for 'frequency' and even then it would be inaccurate because the current is a proxy for the Z-distance to the tip which is then used to convert to a 3D map, which in turn can be visualized.

It is fairly obvious that this is an indirect process so clear the word 'directly' wasn't about 'seeing atoms' but all about the fact that you can make the observations yourself.

Whether you are measuring a current or looking through an eyepiece both are observations. And looking at the resulting image is also an observation.

As opposed to reading about STMs and looking at pretty pictures online or in books.

It's a shallow comment masquerading as an insightful one, the worst way to derail any conversation.

My intent was just to help clear the misconception. Sometimes people say things that sound flippant when they lack an understanding.

The GP's "statement" contained three relevant sentences, two ending with question-marks. I learned from both your answer and its parent, furthering conversation, for me at least.

Read the rest of their comments and see if you still feel that way. As well as the novelty account made for the express purpose of further derailing the conversation.

Yes, agreed. Though I stand by my account of the original comment. (And as such, based on that they may need to go back to troll-school.)

Its a 2D map of the tip position which is a function of the tunneling current over a surface. Its not frequency.

Why are you hung up on these uses of the words "seeing", "showing"? What would you expect as a better alternative.

CA3140 OpAmps also work well.

The comments about 1pF feedback do speak to one of the challenges with feedback stability, where stray capacitance on the proto-board may or may not be present.

Indeed, a 100-Meg feedback resistor is mostly a capacitor. You could think of it as an integrator with DC bias control. This is probably the best article I've seen about transimpedance amplifiers:

https://electrooptical.net/static/oldsite/www/frontends/fron...

You could draw a pretty interesting graph of how the resistance/parasitic capacitance relationship governs which component is dominant at the high end of the resistance range.

Ben Krasnow built his electron scanning microscope back in 2011. I never expected to see that one upped. https://benkrasnow.blogspot.com/2011/03/diy-scanning-electro...

Homebrew STM is a pretty common and simple in principle. I used to have a chemistry prof who would guide a group of high schoolers through building an STM head each year.

Homebrew SEM is probably much more difficult and rare.

The scanning electron microscope project seems far more involved than this one. I submitted the SEM before this one by the way but it unfortunately did not catch on.

Reminds me of a Craigslist ad I saw a few years ago.

U.C Berkeley bought a new electron scanning microscope, and offered the old one free to anyone who wanted it. The ad right there with the free couches, and nicknacks.

I probably couldn’t afford to get it working, but I think about it often.

Could you imagine having a scanning electron microscope in your bedroom?

This account details on what you'd go through if you got one https://mobile.twitter.com/nanographs

Neat.

IIRC, wasn't there a project using a well-sharpened pencil tip?

Also, Applied Science had one in 2011. https://youtu.be/VdjYVF4a6iU

Small past threads:

Home Built Scanning Tunneling Microscope Electronics - https://news.ycombinator.com/item?id=9752215 - June 2015 (9 comments)

Home-Built Scanning Tunneling Microscope - https://news.ycombinator.com/item?id=8884085 - Jan 2015 (1 comment)

Can someone ELI5 the vibration isolation [0] part of it? I kind of get what he's doing, but would appreciate some analogy if it makes sense to make an analogy.

[0] https://dberard.com/home-built-stm/vibration-isolation/

In a nutshell: the vibrations that affect the imaging are pretty high frequency. So to get rid of them he has isolated his whole setup in such a way that if there is a vibration it will be well under the lower cut-off frequency that is part of the measurements. So the whole apparatus may go up or down but that won't affect the measurements. If the whole thing would not be isolated then the rumble from the tires of a passing car or a jet flying over would utterly ruin the measurements.

Especially the vibration damping is nicely done, it is zero contact and has the effect of stopping any beginning oscillation in its tracks.

Incidentally all of the techniques listed there are used for suspensions in LIGO, Virgo and other ground-based gravitational wave detectors, where the problem is the same: stop seismic noise from moving the object under test.

Imagine painting with a paintbrush while standing on a jumping castle with 5 jumping children.

If you have no vibration isolation, it is nearly impossible to draw a very thin and straight line.

(Maybe a bit exaggerated, the vibration analogy is a bit weaker in reality)

Reminded me of this project from 2002 in Geocities:

https://web.archive.org/web/20010417002032/http://www.geocit...

Similar project: http://e-basteln.de/other/stm/overview/

Can we verify the circuitry on a microprocessor with this microscope?

What size features would you be looking to image? STM typically is used for atomic resolution imaging, so the maximum practical field of view is probably in the 10s of nanometers if you have atomistic resolution.

You might be better off with SEM if you need much larger field of view and can live with the coarser resolution limit

Can you image non-conductive surfaces with this technique?

Nope, the technique for that is an Atomic Force Microscopy[1].

1: https://en.wikipedia.org/wiki/Atomic_force_microscopy

And it turns out DIY atomic force microscopes are possible too! (e.g., [1]) It's probably less likely to get all the way to atomic resolution (0.01nm) like a scanning tunneling microscope, but atomic force microscopes can take many types of 1-to-1000nm-scale measurements and are often more practically useful.

[1] https://hackaday.com/2014/04/29/a-diy-atomic-force-microscop...

OR helium ion microscopy, but that is not as widely available afaik

1: https://en.wikipedia.org/wiki/Scanning_helium_ion_microscope

Best you can do is gold plate the object you would like to scan. Sputter coating is the preferred method.

https://en.wikipedia.org/wiki/Scanning_electron_microscope#S...

That’s a SEM which is significantly lower resolution, but lets you zoom in and out across a huge range.

STM on the other hand is for looking at individual atoms so coating a surface is just going to show that coating. https://en.wikipedia.org/wiki/Scanning_tunneling_microscope

That's for SEM. I've never heard of sputter coating used for STM.

You are right, I got those two methods mixed up. It looks like gold sputter coating would be a good solution for the home made tungsten STM tips mentioned in the link.

Sort of?

STM is frequently used to characterize adsorbed molecular monolayers on a graphite substrate.

You're obviously depending on electron conduction to image the sample, but you can image all sorts of things which wouldn't be considered conductive as a bulk material.

Can we add [2015] to the title?

Added now.

This is an amazing project, in so many ways.

My first thought is, the implant business has now got a problem. Soon enough, anyone and their pal will be able, finally, to validate their silicon at adequate scale.

finally? imaging a silicon chip has never been a problem and home-build STMs are not needed.

The geek culture in the US is simply amazing. People build all kinds of miraculous machineries at home, many of which have become world-class products. Some products even changed the history of mankind.

What's even more amazing is that the US somehow keeps this culture despite decades of mockery and bullying from the pop culture and from school, and despite that generations of Americans thought that the biggest events had to be the football games in their neighborhood high schools and the coolest people were queen bees and sports jockeys.

The creator of the linked electron microscope project was a PhD student at McGill (in Montreal) when he built it and (according to his LinkedIn) is currently a startup co-founder in Montreal. So... not sure where US geek culture fits in to this.

Thanks. I falsely assumed that the creator was in the US. Hopefully Canada does not have this strange culture of looking down upon geeks as in the US (so much so that Paul Graham wrote the essay on revenge of nerds, which I couldn't even understand where his emotion came or why he wrote the essay until I came to the US years later).

The football people quickly burn out when nerds are just getting started.

Is this simply a trope made up and amplified by hollywood?

Less smart Americans often have little respect for their smarter compatriots or their smarter compatriot's opinions. That isn't new. Ever hear the term egghead? Modern propaganda about climate and infectious disease have exacerbated the problem.

I think you are stuck on hollywood from 30 years ago. It's cool to be a geek now lose the persecution complex.

Yes, look at all that squashed DNA, lol.

Seriously though, how do we know that is DNA? It just looks like wiggly worms.

And the DNA pic is black and white, but the picture of graphite is in colour. How is it in colour? Is it 'enhanced' with photoshop or something?

You can't actually "see" DNA itself because it is smaller than the wavelength of light. Those groves are 50nm and the wavelength of blue light is about 480nm.

So how then are the images generated?

It uses a technique called Fluorescence Microscopy: https://en.wikipedia.org/wiki/Fluorescence_microscope

You essentially stick some special molecules on the DNA that absorb light in one frequency and then they emit light in another frequency. So you blast the molecules with light of one frequency and then use a dichroic mirror to filter that light out and you only see the emissions and thus you see where the DNA is, but you don't "see" the DNA itself.

Like STM itself what we mean when we "see" something at those length scales is interesting. Scanning Tunnelling Microscopy is like a blind man reading braille - not really "seeing" anything but getting enough info to describe the picture.

source: I used to work in the same lab as Dan. Hi Dan!

This is a useful explanation - thanks!

What does this mean to the value of what we are "seeing"?

The example used before - that it is equivalent to a deaf man seeing a music visualisation - is apt. It is some sort of model, but not particularly close. It might still be useful, of course.

Not "seeing a music visualisation" (was it edited maybe?), reading braille. STM involves sticking a probe microscopically close to the thing-being-scanned, and reading how the surface's atoms deflect it. Which is very close to "literally feeling" the surface, as all "touch" is just electrons repelling each other at a distance - this is just at a slightly larger distance. https://en.wikipedia.org/wiki/Scanning_tunneling_microscope

Maybe a more human-scale-friendly analogy would be "finding the hot burner by moving your hand near it". In STM, each atom is a hot burner. You can pretty accurately figure out the arrangement of burners on your stove without needing to see or touch it.

Molecular biologists aren't stupid. They fluorescent tagged the pieces that get incorporated into the DNA and not into anything else. There will have been positive and negative controls to gain confidence that the tagging worked as expected.

You might want to lose the snarky attitude as it's not a good look when you're really ignorant about the techniques you're sneering at. You seem curious. Just learn without the snark.

EDIT> This is the kind of thing you learn in 1st and 2nd year university biology courses. Especially cell bio / molecular bio lab technique courses.

False colour is pretty much standard for many imaging techniques including STM.

Its not even really false color, its just a look up table applied to the data, which is some equi-tunneling current or height map, don't know exactly how this is done, bit out of my field.

The tip is pointing down, so an increase in current would indicate a decrease in 'Z' coordinate of the sample surface.

DNA extraction is a routine procedure used to isolate DNA from the nucleus of cells.

More here: https://www.sciencelearn.org.nz/resources/2036-dna-extractio...

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