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Hardware Science

Build Your Own Scanning Tunneling Microscope 175

I don't want to spen writes "For all you fans of nanotech out there, a friend just posted me a link to instructions for building a scanning tunnelling microscope, from the University of Muenster. Interestingly, their licensing terms sound open source-ish to me: '(... We grant everybody the right to construct the microscope using the here-published design for private or educational purposes. On these web pages all necessary diagrams, drawings, material descriptions and software-source-codes are published for free access. While granting the right to build the microscope we make it mandatory that new developments, improvements or other applications of our design are also made openly available for private or educational purposes...)'"
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Build Your Own Scanning Tunneling Microscope

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  • by gerrynjr ( 662919 ) on Saturday January 03, 2004 @10:04PM (#7870429)
    come on! At least write it in java....

    Seriously though, looks like a great summer project.. Not to mention my college will now have a SEM because of these plans :-D
    • Seems like the time to get a new pair of really small tweezers. But wee, seriously, yes, this is cool. This is a great project for "young" people and such - I'll propose this to my group in the Norwegian Council for Young Scientists [ungeforskere.no] right away! Great that someone really makes a framework for others like this, by giving people help to help themselves. Hopefully, we'll be seeing more stuff like this in the future. I miss the LEGOish manual though.
      • Re:Visual Basic? (Score:4, Informative)

        by Anonymous Coward on Saturday January 03, 2004 @11:49PM (#7870801)
        Maybe you should read it a little closer. This is a summer project for rich and technically competent high schoolers, or grad students. This is not cheap. And when it comes to making tips I think it's great to have kids playing with tubs of KOH.

        And it's not SEM, it's STM. Sem is great for making pictures of insects and what not, STM is great for tracing out the p-orbitals of graphite. BIG difference (not your error, but as long as I'm clarifing, why not hit that too).

        Propose a sputtering chamer or a PVD chamber, they'd probably be much cheaper to build and can be used to make other stuff. Which then one could look at with either an SEM or STM if one chose.

        Goto industrial and university auctions too. I've hear tell of people giving TEM's away to whomever was willing to transport them (not that an isolation pad on which to set it is within the means of Young Scientists). But still.
  • I work in a plant growth research lab, and we built one of these to get real time images of protoplasts (plant cells in culture). It was cheap, and produces what I found to be suprisingly excellent-quality images. Of course, we also got a hundred thousand dollar Bausch & Lomb scope to do more "complicated" work...
  • by seanvaandering ( 604658 ) <sean.vaandering@ ... m minus math_god> on Saturday January 03, 2004 @10:06PM (#7870437)
    Okay the instructions are in English - nice. The diagrams are in German? Need a little help here...
  • ^^

    seriously, the open sourcish license is interesting. It would work very well in an academic setting, which is analogous to actual OSS: people creating "products" with their primary goal not being money, and the GPLish license prevents it from being incorporated into proprietary, commercial products.

    I don't know if you can do anything meaningful in your mom's basement with the STM kit, but interesting nonetheless.
  • >> from the article:
    The software was written in Visual Basic 6 for Windows

    Great! But I wanted to control the STM from my linux box :\
    It already controls my lights, coffie maker, telephone, network, CD player...

    NeoThermic
  • omg! (Score:5, Funny)

    by niko9 ( 315647 ) * on Saturday January 03, 2004 @10:11PM (#7870460)
    A hardware desging, in the GPL style, released to man for his education and enlightenment?

    You mean this is not like, say for a example, some greedy physician who comes up with a slightly different way of suturing someone with existing tools, patenting said technique, and then demanding worldwide royalties????

    The end is near! /faints/

    --
    • These guys don't know how the rules work.

      If they put out the design publicly, and they don't have a patent, anyone can build one based on their design, for any purpose. Copyright protects their design document, but does not affect what anyone who legally obtains the design document does (e.g. builds an STM).

  • HA HA!! (Score:1, Offtopic)

    by pair-a-noyd ( 594371 )
    My httrack beat your /. effect!!

    I win!!
  • by frovingslosh ( 582462 ) on Saturday January 03, 2004 @10:14PM (#7870472)
    the measurement computer must have a free slot for ISA cards.

    Well, I still have this covered, but not many of my friends do.

    • Bug them for a diagram giving instructions on making ISA slots out of dilapidated copper and Scotch tape, then.
    • by SirTreveyan ( 9270 ) on Saturday January 03, 2004 @10:50PM (#7870618)

      The design as given requires a ISA slot because of the type A/D converter card they selected. If you do not have an ISA slot available, I am sure a PCI based, or even a USB based analog to digital converter can be found. It would probably be a good idea to change the A/D, as the one used has a 100khz refresh rate. I am sure that there are cards out there that refresh at a much quicker rate, thereby allowing improvements in other areas of the design. Just be aware that the software would have to be modified because of the different card, but that should not be a difficult matter for anyone attempting this project.

      • Why couldn't I just use my soundcard line inputs? Not trying to be an asshat here, just reminding people that modems and soundcards basically *are* A/D devices. If you have the $$$ to spend, you can find A/D cards here, [ni.com] they supply pro stuff. Yeah, I'd like to try this under Linux, but I need to ask: does anyone know a good way to re-code the VB into C/C++? This is not the kind of project I normally consider, but its just too damn interesting. Thanks.
        • by frovingslosh ( 582462 ) on Sunday January 04, 2004 @01:52AM (#7871468)
          The technical answer has to do with lots of issues, like most sound cards being for AC signals and the input not so great for DC signals. The simpler answer just asks would you do surgery with a chain saw?
        • There are several reasons why you would not want to use a sound card's line inputs. One the most important is that a sound card's refresh rate is not continuously adjustable over the range which it can operate. I have not messed much with sound cards lately as ripping CDs and working with sound is not what I am into, but I seem to remember that sound cards sample as certain predetermined rates like 8k/sec, 16k/sec, 22k/sec and 44k/sec. I am sure sound cards can sample at higher rates, but if you need to

      • www.DigiKey.com has a great number of A/D chips, many under $5. If you can handle a soldering iron and can read the spec sheet, you should definitely consider it.
  • by mukund ( 163654 ) on Saturday January 03, 2004 @10:15PM (#7870475) Homepage
    My question may seem weird due to my ignorance. Is it possible to use such a microscope to find the structure of say.. the HIV virus and its chemical composition? Secondly, how are such small structures located/found due to the huge spatial distances involved?
    • by QuantumG ( 50515 ) <qg@biodome.org> on Saturday January 03, 2004 @10:30PM (#7870538) Homepage Journal
      no. To find the 3d structure of a protein or a virus you need to be able to crystalize it and then use a technique such as xray crystalography or NMR. There are some new techniques being developed based on mass spectography that can determine the structure of proteins that cannot be crystalized, but they're in their infancy. An STM simply can't be used, because the sample must be able to conduct a current (ie, it has to be a metal or something placed on top of a metal). Preparing samples for an STM is much like preparing samples for an electron microscope, you need to infuse the sample with a conductive material (usually gold) to be able to see it clearly.

      Atomic force microsopes on the other hand can do some very neat work with small organic particals, but seperating something like an HIV from solution is still difficult, and usually involved crystalization.

      • True, and to relate the above back to the main topics of this site, the reason we need to use crystallography to determine the structure of a protein is that we currently possess nowhere near the amount of computing power necessary to derive a protein's structure simply from the sequence of amino acids that make up the protein.
        • by QuantumG ( 50515 ) <qg@biodome.org> on Saturday January 03, 2004 @10:52PM (#7870627) Homepage Journal
          Depends on the size of the protein, but unfortunately you're right for most interesting proteins. There are hybrid computational modelling + mass spectrography techniques that can reduce the required computational time by orders of magnatude. When peptides fold up into proteins they make covalent bonds between the aminoacids. When you're doing a computer simulation you can say something about which bonds are more likely than others (and this can reduce your run time to less than blind search) but you can't say with any certainty which aminoacids are bound to which. What these hybrid techniques do is cut up the folded protein into small molecules (5-6 aminoacids) and then messure the mass. From this data you can tell if there are certain crosschain combinations. For example, you can see that there is a Cysteine-Asparagine bond and if there is a Serine-Proline bond or whatever. Armed with this information you can remove a lot of possibilities from your search space.
      • Actually, NMR can be used to find the 3d structure of a molecule in a solvent. x-ray crystalography it used on a crystal and therefore does require a single (perfect) crystal for detailed data (i.e. what do the individual molecules in the crystal look like) or a powder for simple distance data (i.e. the distance between two heavy atoms in a crystal).

        You may also be able to use MAS to find information about a crystal via NMR but I have never heard of that being done (havent looked lately). NMR crystalography

    • This type of microscope requires a target which will conduct electricity. That's why images are typically of gold, semiconductors or items which have been electro-plated.
    • by Dr. Null ( 737669 ) on Saturday January 03, 2004 @10:43PM (#7870593)
      I am not aware of any of any instance of a large molecule whose structure was deduced from a scanning tunneling microscope. Things like proteins, enzymes, and viral particles are most generally probed by growing them into crystals and a analyzing their x-ray diffraction patterns. The big problem with this technique is that big molecules are hard o grow into crystals (thus all the grow protein crystals in the micro gravity of orbit effort) Nonetheless, a Scanning tunneling microscope is VERY COOL, and within the engineering capabilities of a dedicated hobbyist. Heck, you can now buy a complete Scanning tunneling microscopes for 20K; pretty cheap for a high-end piece of laboratory equipment. The real trick is to get the stage into a hard vacuum at cryogenic temperatures. Who will be the first person to spell out LINUX in Xenon atoms on a nickel substrate? I will donate money to that cause By the way, in college I used to produce atomically sharp needles for field emission ion sources just by burning tungsten wire in a propane torch. That should be an easy way to make probe tips
    • by Compuser ( 14899 ) on Sunday January 04, 2004 @01:55AM (#7871479)
      I am probably quite qualified to answer your
      question seeing as I do STM research for a living.
      Your second question is easier to answer, so I'll
      do that first:
      there are two ways, either you put down enough
      of them to assure there will be a molecule in the
      range of your scanner whereever you approach
      or you use some other technique like lithography
      to make small structures then another technique
      to deposit your molecules near those structures
      then (if you got the microscope that allows it)
      position your tip optically near the structure
      and spend days on looking around with STM until
      you find it.

      Now you first question. STM can be used to find
      some structural info from large molecules. My lab
      has done some research on nanotubes and you can
      get atomic resolution on those and then determine
      their helicity. People have also imaged bio stuff
      and for some smaller molecules have seen the
      structure. Even DNA has been imaged. That said,
      STM is not a great structure probe, it is a great
      probe of electronic states.

      Last word of warning: people rarely realize that
      STM in air is not going to tell you anything
      that you can rely on physics-wise. The reason is
      that all surfaces exposed to air are covered in a
      thin layer of water which makes the interpretation
      of data hard. What they show on that page is a toy
      though well-thought-out and maybe even useful to
      some. Seeing atomic steps on gold and "atomic"
      resolution on HOPG is not hard, just don't hold
      your breath for something like atomic resolution
      on gold, or silicon, or anything else really.
      For that you at least need a UHV system.
      Cheers.
      • Well, asside from making sure you use vacuum-compatible materials that won't harbor too much gas, it's not that hard to make a vacuum enclosure. I've bought lots of vacuum equipment off eBay, and scavenged old parts from places I've worked.
        (sitting 1 meter from a rebuilt Leybold Turbovac PT 50, and other parts)

        I recall the ancient SEM at the first place I worked. 1960s equipment. I got okay images after it was cleaned up, and was only drawing vacuum through an old piston-pump. Ex-refridgeration pumps can d
        • This is gettig offtopic but...
          Building a UHV system (10^-10 torr type vacuum)
          is expensive though not hard. Part of it is that
          you'll need quality metal seal flanges to connect
          parts of your system, another part is that you
          need an ion pump because turbo and mechnical
          pumps introduce too much vibration. Of course
          if you got the money you could also dump it all
          inside a liquid helium dewar and be done with
          cryopumping alone.
          If you are scavenging equipment then look for
          a mechanical, a turbo and an ion pump (you'll be
  • Prions (Score:2, Interesting)

    by Mr Bubble ( 14652 )
    Can a tunneling microscope see prions?
    • Re:Prions (Score:2, Informative)

      by a-aiyar ( 528921 )
      No, but you can visualize prion proteins within intact cell with a conventional electron microscopy. I kid you not. Here's an article [nih.gov] with some really pretty pictures of prion proteins trafficking in cells.
  • Sad face? (Score:5, Funny)

    by Polyphemis ( 450226 ) on Saturday January 03, 2004 @10:22PM (#7870510)
    Interestingly, their licensing terms sound open source-ish to me: '(

    heh, did anyone else quickly glance at that and think he was making a sad crying face because it sounded open source?

    "Uh oh! It sounds like open source! :'("
    • by Anonymous Coward
      Actually, I'll one up you. The only reason I read the comments was to find out why he made the sad crying face.
    • No, but I did wonder when you wrote :'(" why you drew a guy with a beard smoking a cigar...
  • open source-ish? (Score:4, Informative)

    by 49152 ( 690909 ) on Saturday January 03, 2004 @10:30PM (#7870540)
    I dont think so

    With BSD or GPL style licenses you are actually allowed to use the copyrighted work in an commercial setting, just not to sell it. For instance a commercial company might run their web server using GPL licensed software.

    With this not only do they retain the exclusive commercial rights, but the license might in fact be read as an attempt to force you to turn over any improvements on their design.

    So if you make an improvement, does this mean that you have implicitely granted the University of Muenster the rights for commercial exploitation of your own improvment by accepting their license in the first place?

    This does not sound "open source-ish" to me, it sounds like out right theft.

    PS: Please ignore any bad spellings/grammar in my english or at least be polite when telling me ;-)
    • Wrong.
      'Openly available' != 'turn over to the University of Muenster'
      • 'Openly available' != 'turn over to the University of Muenster'

        Perhaps not, but I dont think that license was very 'Open Source' anyway. It is however very much 'free beer'.
    • by Anonymous Coward
      *sigh* Another RMS brainwashee.

      You're one of those people who when a restaurant gives a free lunch gets pissed off because you can't sell it to another customer.

      There is no out right theft. You don't have to build one of these STM's. If you want to, then follow the license. Otherwise go somewhere else and shut up. This group is offerring you something for free. Just because they aren't also giving you the keys to their car or their house doesn't make them evil.
      • Re:open source-ish? (Score:2, Interesting)

        by 49152 ( 690909 )
        Did you bother to read what I wrote? No? didnt think so.

        I dont mind that I cannot sell their invention, of course not. But I do mind having to give up for free any improvements I make unless *they too* give up this right.

        This is what "Open Source" is all about, freedom of information not "free beer".
    • Come on, think about GPL requirements for using and redistributing GPL'd code, then remember that these guys are offering the design and software for a device, then compare. They release the design and software (and any device based on the design) for public or private use (I wish I could be certain about the translation of the German - there's an odd passage about a view of the circuit board "with eagle"). If you improve the system, they want you to return the original favour. I don't think that proposa
      • Except that nobody can build these and sell them for just enough to keep operating, giving people a relatively inexpensive STM device.

        With the GPL they not only could do that. But they could improve the device (perhaps porting the software to linux and replacing the card with a PCI Version for starters) and distribute that improvement whether this initial project decided to or not.

        That reveals another big disadvantage. With the next server upgrade at the University this will likely disappear (like most
  • I think a similar thing was done with robots that carried out part of the human genenome project. Sorry I forget the group that put the plans out on web. Any how, there is certianly a demand for scientific instruments that can be assembled for relatively low cost. A good thing for universities in developing countries, that can't afford the cost of brand new equipment. I saw a pH meter made of the carbon rods from D size cells made in India. A lot of labs in developing countries either buy second hand equipm
  • by MajorDick ( 735308 ) on Saturday January 03, 2004 @10:48PM (#7870612)
    I mean this is cool, bet really the cost on older electron microscopes is pretty low (under 2k) Heck theres a phillips 500 for sale on Ebay for $1000 right now. I've often thought about buying one, but dont have 3 phase in the house and the garage is a little damp.
  • by Anonymous Coward on Saturday January 03, 2004 @11:07PM (#7870679)
    Despite what they call it in English (University of Muenster), the proper name is the Westfaelische Wilhelms Universitaet. Even though I am an American, I studied there for a semester.

    Muenster is a wonderful college town, as well as a place of historical significance (30 years war ended there). The hospital associated with the university, and thus the medical program, are well respected across Europe. (Comparible to Mayo / Johns Hopkins / Mass. General here in the US).

    Anyway, while it is surprising to see this on the front of /., it isn't a surprise to see good things from Muenster. It is one of those wonderful little secrets - a top notch place few know about.

    Posting AC because I believe in privacy on the net ;)
  • From FSF [gnu.org]

    ``Free software'' does not mean ``non-commercial''. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important.

    OSI [opensource.org] talks a lot about including open software in the commercial world.

    Closing free software to commercial entities is an idea roundly rejected by modern free software thinkers.

  • More STM info (Score:5, Informative)

    by apirkle ( 40268 ) on Saturday January 03, 2004 @11:32PM (#7870758)
    There is a similar reasonably well-documented homebrew STM [e-basteln.de] that was built by a guy named Jurgen Muller. His site is pretty interesting, and well worth the read.

    Obviously there are a lot of articles on STMs in various academic journals. If you're at a university, you might start by searching in Reviews of Scientific Instruments and perhaps the Phys Rev journals.

    I was involved with a STM project for a while, and our conclusion was that the 3D piezo setup is quite fragile, and extremely difficult to isolate from vibration, etc. It seemed that a better design was a so-called slip-stick walker, which uses a stage that slides on smooth rails. A tube of piezoelectric ceramic is attached and driven in such a way that it creates a series of small, sharp forces on the stage that momentarily break the static friction between the stage and base, causing it to move in small steps.

    This stage is used to approach the sample to the STM tip, which is mounted on another piezo tube, and can be deflected laterally and vertically in order to do a raster scan of a small area of the surface.

    The limitation to this method is that you can't scan a very large surface area. You can add a second "walker" unit underneath the first one so that you can move the sample from side to side in addition to moving it towards/away from the tip, so this would allow you to scan a stripe across the surface.

    To get full 3D control, there are several designs called "beetles" (IIRC) that are described in the literature, which use a somewhat similar technique that allows more control.
    • Re:More STM info (Score:3, Interesting)

      by Compuser ( 14899 )
      Beetle design, also known for its creator as the
      Besocke design is not unique in allowing full
      3D approach positioning. It does have many advantages
      like farly good rigidity, thermal compensation and
      ease of assembly.
      There are designs which are even better than
      slipstick, such as the good old inchworm design
      and its offshoots, especially ones designed for
      low temperature operation (some are patented).
      Even slip-stick isn't limited to beetles. Another
      design was patented early on by Lyding and is also
      thermally compen
  • Vibration damping (Score:5, Interesting)

    by fermion ( 181285 ) on Saturday January 03, 2004 @11:36PM (#7870769) Homepage Journal
    Of course, the most important component for any optical experiment is the Vibration Proof Table(TM)(patent pending). We have several of these using your choice of technology. The cheapest is the Immovable Mass (TM). The downside to this is that it is nearly impossible to ship. Another technique is hanging the apparatus on the Massless String(TM) from a Nearly Immovable Mass(TM). This requires not only an onsite visit by our service technician, but two years advance notice to acquire the material. Finally, we have the Completely Decoupled Environment(TM), in which we put the apparatus in the Perfect Vacuum(TM), and keep it away from all walls with a Leak Free Perfectly Damped Magnetic Field(TM)(patents pending). Unfortunately, though this system is relatively cheap, getting new samples on the 'scope is quite impossible.

    We assure you, however, that hanging the scope from a thin scaffolding using light springs, and then attaching the entire setup to a huge piece of granite will not be sufficient.

    On a more serious note, an STM is really easy to build, but really hard to make work. There has been more than one physics graduate student that has entered perpetual grad school limbo trying to get one of these to work. The vibration damping is just the start. Learning to etch the tungsten probes so that you get the necessary few atoms at the end is quite an ordeal. And then attaching the probe without allowing the tip to even come close to any surface. And then calibrating the piezoelectric so that the tip will be very very very close to the sample, but never touch it. You will go through 100 hand etched probes before the instrument is even grossly calibrated.

    And then measuring the gap current. You learn what kind of noise a power supply really has. Getting a noise low enough so that a signal is discernible after amplification requires a power supply the likes of which few has seen. And then the noise that introduced by the amplification process. This are not your ordinary op amps. I shudder to even think about building a board that quiet.

    But have fun, and remember us for you optical table needs. We are, after all, the only one who sell the genuine and otherwise real and purchasable Vibration Proof Table(TM)(patent pending).

    • Actualy, when I did it as an undergrad none of this was a huge problem. It took me one day to move the thing to the basement and set it up directly in the foundation (locating a relatively low vibration area with a laser and some Hg observing the beam to see how large its vibrations were).

      Then about another day to learn how to cut the Pt-Ir needles to be atomic (this isn't that hard, a wire cutter worked). If you think about it there is probably a single atom at the bottom no mater what (there has to be one

      • Re:Vibration damping (Score:4, Interesting)

        by Compuser ( 14899 ) on Sunday January 04, 2004 @02:19AM (#7871543)
        a. Please tell me you got an F for your efforts
        as an undergrad. I say this because the very
        essense of tunneling is that it falls of as an
        exponential, not as a power law.

        b. I assume you were doing STM in air or else
        moving a setup downstairs would have taken at
        least a week to rebake the vacuum chamber. Now
        in air, you have a thin layer of water on the
        surface which surprisingly makes it easier to
        stabilize a junction.

        c. Tips aren't quite some much of a problem, I
        agree with that, especially since very good tips
        can be bought commercially. And cutting a wire
        may work well for metals and semiconductors.
        Attaching a probe is usually easy because the
        only part you can't touch is the very end.

        Responding to original poster:

        d. There is no need to calibrate the piezo to be
        able to tunnel, that's what a feedback loop is for.
        You do have to have an idea of what parameters to
        use so it doesn't ring.

        e. In fact an ordinary op-amp will do fine and a
        clean dc supply from any decent manufacturer
        will do the trick. Look at bio and chemistry
        literature dealing with patch clamp applications
        for good references on more sophisticated designs
        but it aint rocket science. The one hard part is
        to make sure you put your setup far from any
        60 Hz source and have no ground loops or even
        no weak grounds anywhere in you setup.

        Lastly, the hard part about STM is getting
        meaningful data. You typically get junctions that
        aren't so good and you need to be able to tell
        whether it is the tip or the surface. Generally
        to do that you need to do this for a few years and
        build up and internal reference for which type
        of crappy junction corresponds to which problem.
        Then getting a good junction and some data becomes
        easier.
  • should have landed a few minutes ago - cant find any news.
  • by core plexus ( 599119 ) on Saturday January 03, 2004 @11:49PM (#7870806) Homepage
    ...my study of the role bacteria play in geology, and in particular (no pun intended) in the formation of valuable precious metal deposits such as this: Alaska Bugs Sweat Gold Nuggets [alaska-freegold.com]

    If nothing else, it might be cool to build one just to look at stuff, and I finally have a use for that ISA slot.

    -cp-

    President Bush to Liberate Alaska! [alaska-freegold.com]

    • Interesting field. We were given a presentation on gold abd bacteria early last year. I also was told of work looking at gold uptake in plants to assist with gold prospecting. I asked if it was passive or active (like silicon in some plants). Not sure was the reply.
  • by Ray Radlein ( 711289 ) on Sunday January 04, 2004 @12:43AM (#7871127) Homepage

    For a horrible, horrible moment, I read the headline as "Build Your Own Spamming Tunneling Microscope."

    Just think what horrid new forms of viral marketing a research tool like that could help develop.

  • by drfireman ( 101623 ) <<dan> <at> <kimberg.com>> on Sunday January 04, 2004 @01:38AM (#7871413) Homepage
    If we use the FSF's mode of describing things as a point of reference, this is probably an open source project, but not a free one. If it were a software project, it would violate the very first of the freedoms the FSF considers essential (look here [fsf.org]) in that it restricts who may use it for what purposes. Whether or not they can meaningfully impose that restriction is a separate issue.

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