Molecular Photography

By JoAnne Hewett | November 3, 2006 3:46 am

How would you take a photograph of a molecule in motion? You can’t just go to the camera shop and pick the appropriate device off the shelf. You’ve got to build it yourself! So, what type of device should you build? Well, an average length for a molecule is 1 nanometer (10-9 meters), so you would want a part of the electromagnetic spectrum with a small enough wavelength to be able to discern (i.e., scatter off) an object that size. X-rays, which have wavelengths of approximately 0.01-1 nanometers, would do the trick. And you don’t want blurry shots, so you would want the X-ray pulses to be rapid enough in order to freeze the ultra-fast molecular motion — something like 10-(9-10) seconds between pulses would work. And the X-rays should be bright (high intensity) — nothing worse than a dingy picture.

Sounds like a job for an X-ray free electron laser! The world’s first such device of this scale is being built, right here at SLAC. We had the groundbreaking ceremony a few days ago, so the project is now officially underway. Lots of dignitaries were here to shovel the dirt and give inspiring speeches. They were Department of Energy Under Secretary of Science Raymond Orbach, Congresswomen Anna Eshoo and Zoe Lofgren, Congressman Mike Honda, Stanford University Provost John Etchemendy, and SLAC Director Jonathan Dorfan. Last, but not least, the Stanford University Marching Band performed at the event. They have a reputation for being a rowdy bunch (the band, that is) — the University has gone as far as to ban them from performing at football games this year — but they were appropriately toned down (for a band, that is), and added just the right air of festivity to the event.

So, just what is this X-ray laser going to do? Literally, it will take photographs of molecules and reveal their structure. Current X-ray sources primarily give a static picture of materials averaged over relatively long time scales. This new machine will make movies of fast-moving chemical reactions, capturing each movement instantaneously in a frame; it can also determine the structure of a single molecule or small clusters of molecules, and study new states of matter called warm dense plasmas, and perform a vast array of other scientific feats. For instance, it will be possible to record time-resolved images of chemical reactions, to the point of following the change in the chemical bond as the reaction proceeds. Indeed, it seems that it can do almost anything and that everyone is interested in it. Chemists, biologists, physicists, drug companies, even historians. You name it! Which is why the DOE is plunking over roughly $400 M for the project.

At the groundbreaking event, Stanford Provost John Etchemendy made an interesting comparison. He told the story of Eadweard Muybridge, who engineered and developed photographic equipment of his time. Under the employment of Leland Stanford in 1872, he was the first to take a picture of a galloping horse. Previously, during the entire history of humankind, it was thought that a galloping horse kept at least one, if not two, legs on the ground. Muybridge’s photographs comprised the first instance that a galloping horse’s movement had been frozen. And what did humankind learn? That galloping horses have all four legs simultaneously off the ground. May not sound like much to us today, but just imagine 130 years ago.

This wonder machine is called the Linear Coherent Light Source, or LCLS. LCLS will use the last third of the linac to create tightly-focused accelerated bunches of free electrons (here, free means not bound to atoms). Bunch compressors are being installed in the linac to squeeze the electrons into 20 micrometer sized, intense,pulsed packets. These electron bunches then leave the linac and enter a series of undulator magnets. To my understanding, the undulators make the electrons wiggle and thus change course, during which they give off X-rays via synchrotron radiation. And the undulators are built in such a way as to make the X-rays coherent, with a wavelength of 1.5 Angstroms (0.15 nanometer). At the end, the world’s most intense, fastest pulsed coherent (like a laser) X-rays are beamed into a suite of experiments. Cool!

Lastly, how do us SLAC particle physicists feel about turning our laboratory over to the Basic Energy Science division of DOE? I would be remiss if I did not mention this… Well, first of all, we are tickled pink that our linac will continue to produce groundbreaking scientific results. It is just another phase in a long history of outstanding science performed at our laboratory. I must also be honest and admit that there is some apprehension that particle physics will become marginalized at the lab. However, strong leadership and a thoughtful layout for the transition will ensure that this does not occur. SLAC has a very talented particle physics workforce, and current and future particle physics projects do and will depend on it!

  • PK

    That’s very exciting news, I can’t wait to see the pictures.

    When you first asked the question of how to image a molecule, I thought about a lens with negative index of refraction (this can be made using meta-materials). Such a lens can image below the diffraction limit via evanescent waves. But you’d have a problem with the timescale of the imaging, I reckon.

  • Quasar9

    Hi JoAnne, Congrats to SLAC
    I really would have liked to have been there
    but glad I can count on you keep me updated here.
    That second photo looks like a lot of
    ‘excited’ particles & molecules dancing in the air.
    Is it from the latest Village People release?
    Hope you are having fun! and,
    no, I haven’t forgotten those seeds for next years crop

  • Pingback: Zooglea

  • Jeremy

    Congradulations SLAC!
    reminds me of the Advanced Photon Source at Argonne National Lab that images the insides of live insects with powerful x-rays. Slightly before they die of radiation poisoning that is.

    Anyway, sounds exciting!

  • Alexey Petrov

    It’s great to hear that particle physics will be an active part of the Lab in the future, at least theory and astro… Rumor had it that the leadership of SLAC didn’t even want to consider “local” continuation of the experimental particle program in B-physics (i.e. super B-factory) — is that true?

    Actually, X-ray laser is not the only technique for this. There is also a technique called “Atomic Force Microscopy” that is used for “taking pictures” of the atoms… but the device is really tabletop (located in a lab across a hall from my office)…

  • nigel cook

    Jeremy, what insects did they x-ray? American cockroaches allegedly can only take 67,000 R, but German cockroaches are hardier and will take 90-105,000 R, see

  • Chris W.


    Sorry to throw in a blog administration question, but why is select/copy-and-paste from CV posts disabled under Internet Explorer? (I haven’t tested Firefox or other browsers.)

    To grab a paragraph for inclusion in an email, as I just did, I have to view the page source, locate the relevant paragraph in the HTML code, and copy it from my source viewer.

    I believe this has been an issue ever since CV came online.

  • JoAnne

    Chris W: Wow, I have no idea. Sounds like something we should fix though. Unfortunately, I am barely beyond point & click, so I’m the wrong one to be having this conversation.

    Alexey: Precision measurements and heavy flavor physics, as important as they are, were given the lowest priority on both the EPP2010 and P5 roadmaps. I believe the particle physics community is just not willing to pay $500 M for a super-B-factory. That kind of funding is not up to the SLAC director, that brand of science would have to be a priority of the community and DOE.

  • Aaron

    free electrons

    Free electrons?! Where?! ;)

  • Aaron

    On a more serious note, how do you plan to use this new-fangled contraption for making movies? I thought that shooting a cloud of molecules with a high-energy x-ray beam was like shooting a cloud of gnats with a fire hose — you could get one good still frame, but then the reaction would be blown apart. Is this one of those dealies where you keep running the same reaction over and over, taking shots at 1ms, 2ms, 3ms…? I don’t understand how this could work well with reactions involving more than two molecules!

  • JoAnne

    Hi Aaron,

    I am not an expect on this, but I think perhaps the trick is that the X-ray pulses are just plain super fast, being just a nanosecond apart. Or perhaps since LCLS is at the high energy end of the X-ray spectrum, perhaps they don’t disturb the molecules that much as their wavelengths are a couple of magnitudes shorter than the molecular size. Just a couple of thoughts…

  • N. Peter Armitage

    >I thought that shooting a cloud of molecules with a high-energy x-ray beam was >like shooting a cloud of gnats with a fire hose — you could get one good still >frame, but then the reaction would be blown apart. Is this one of those dealies >where you keep running the same reaction over and over, taking shots at 1ms, >2ms, 3ms…?

    Aaron, you got it… ‘cept it’s more like 1 picosecond, 2 ps, 3ps!


  • Jeremy

    Nigel Cook,

    I believe they imaged beetles. In my opinion, the scientific merit behind their work is slightly clouded. They went outside the lab in the woods and gathered up whatever bugs they could find and stuck them in the beam. One of the objectives of the experiment was to see ‘how long it would take for a bug to go berserk’. But, because there are no activists protecting the rights of dung beetles, there was no problem. I think one of their images appeared on the cover of Science a few years back…

  • Dave

    AFM, as well as Scanning Tunneling Microscopy, are both good tools for atomic imaging, but both have some major constraints – the first of which is their constraint to solid substrates, and only the surface of those substrates. Also, neither technique has the ability to actually take a “picture” of the surface, but rather makes a topological map of the region based on current differences and tip deflection. I’ll never forget the first time I saw an AFM image – imagine getting a B.S. degree in Chemistry and never seeing an atom other than through X-ray crystallography!


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