resistance is futile

August 31, 2006 at 9:47 pm | | everyday science, lab safety, nerd

I needed to illuminate a vial of frozen dye solution with a laser and view the fluorescence. But I didn’t have enough hands to hold the vial, turn off the lights, and hold a long-pass filter (to block the excitation light). So I thought, What would W.E. Moerner do (WWWEMD)? Suddenly, I knew what I had to do: tape the filter to my safety glasses. Genius! (In the past, W.E. has encouraged me to tape diffraction gratings to my glasses and look in the microscope.)

Figure 1. The contraption.

This worked like a charm: I simultaneously protected my eyes and blocked the excitation light with a wink of an eye.

Figure 2. My friends call me “seven-eyes.”

Feel free to use this idea next time you get sick of holding an optical filter in front of your eyes. Just send the royalty check to me.

Why so hard, Mr. Gaussian?

August 31, 2006 at 12:14 am | | everyday science, software

I’ve been doing some electronic structure calculations recently, and this is a job for Gaussian03. Sweet Gaussian. It’s a fine choice for electronic structure calculations, but there are some true oddities.

1. The program is probably the most popular suite for solving quantum mechanical calculations. Thousands of chemists use it and pay through the nose to do so. However, it is almost completely undocumented. For example, see the description of the transition option under the Density keyword (Figure 1). What is the transition density? Ought I know? Basically, do any calculation with any method other than B3LYP/6-31G and you’re screwed.

Transition=N or (N,M)
Use the CIS transition density between state M and state N. M defaults to 0, which corresponds to the ground state.

Figure 1. Out of context? no. See for yourself.

2. Why does it crash? I realize it’s a complicated system and lots can go wrong. But, why doesn’t the output file give any useful information about the system failure. It’s a smart program. It should know why it failed and speak its mind. Figure 2 shows one of my favorite error messages. Of course, there is no content about such errors in the documentation.

Erroneous write during file extend. write 172031 instead of 4096
Write error in NtrExt1

Figure 2. Actually, I know what this error is. The computer ran out of hard disk space. But, it wasn’t easy to figure out. Try googling the error message. You’ll find a bunch of people trying to figure out what NtrExt1 means.

Why isn’t there a wiki-gaussian? I don’t know, but I hope I’m not banned for asking.

dylan, eat your heart out

August 28, 2006 at 2:59 pm | | cool results, everyday science

Dylan at tenderbutton is always posting about his beautiful crystals. But I’ve one-uped him, because I did it the lazy way and with no usable results: I made crystals of my dyes by letting the waste beaker dry in the hood. I know, that’s a lab-safety no-no, but it was a mistake. And the results were cool!

Figure 1. The crystals under room lights.

Figure 2. The crystals under UV illumination. Note the heterogeneous fluorescence, a neato result of mixing a bunch of dyes and solvents together and letting evaporation do all the work.

Is that Pong on your dress, or are you just happy to see me?

August 25, 2006 at 3:12 pm | | stupid technology

Submitted without additional comment, because nothing sarcastic I could say would do this baby justice.

Powers of Ten – Prepare for the Mind-Melt

August 24, 2006 at 8:29 am | | science and the public, wild web

Drop everything, hit play.

I first saw this movie, as a wee first year graduate student while killing sometime in the Green library media room. If this doesn’t inspire you to be a scientist, I dont know what will. A high-quality DVD is available from the Stanford media library. From the official site:

In 1977, Charles and Ray Eames made a nine-minute film called Powers of Ten that still has the capacity today to expand the way we think and view our world …

And then there were 8…

August 24, 2006 at 8:15 am | | news, science and the public

Well, the IAU has now decided that Pluto is a planet no more. Resolution 5A passed, which officially demoted the now “Plutonian object.” I have to say I’m very pleased with the outcome. As a scientist, nothing gives me greater pleasure than making children cry. I wonder if it’s too late to get a refund on the New Horizons program…

If I may, a tribute to the far-off, icy land:

Folding in Style

August 23, 2006 at 10:19 pm | | nerd, news, science and the public, science@home, software, wild web

The folding-at-home package has been ported to Sony’s much anticipated PS3 console. The point? None! But, it’ll make Vijay’s group happy and its always nice to see some of our peers get street-cred in the popular media. I hear their groundbreaking cell architecture is a ~10x improvement over your typical PC!

Ah, the irony – this is probably the only software out there that can leverage the PS3’s sweet sweet cpu cycles. Now, if I could only frag more of those proteins … sigh … here is some eye candy:

The official press release from Folding at Home and some coverage from Engadget.

future of biology

August 23, 2006 at 4:40 pm | | news, science and the public

Neal sent most of the Chidsey Lab a link to an interesting Charlie Rose interview from last night. It’s loosely about the great Biology discoveries of the past – Darwin, Watson, etc., the merging of chemistry with biology in the 20th century, and the future direction of biology. Check it out – an hour long, but definitely worth watching. Thanks go to Josh “da Man” Ratchford for forwarding it.

Charlie Rose Interview

Relatively Awful

August 23, 2006 at 1:58 am | | cartoons

Let’s find the most poopy cartoon involving Einstein. Get a wiff of Figure 1 for some truely poopy cartoonin’.

Figure 1. Look at me.

What is wrong with Einstein’s arms? Is he wearing a burlap sack? Is that a chalkboard? I don’t even want to start, baby, with the dialog.

So, the challenge is to find a worse cartoon. My numbers suggest at least 10^3 terrible Einstiens out there. Find them and post them. If you’re not a member, place the link in the comment section, and I’ll make Kendall post it for you. Happy hunting and godspeed.

First Empirical Detection of Dark Matter

August 21, 2006 at 10:48 am | | nerd, news

Well, after giving everyone a taste of what is to come today, NASA has finally let the cat out of the bag. During the observation of a collision between a pair of clusters, the observers were able to resolve the separation of baryonic and non-baryonic matter by comparing the luminous and gravitational profiles.

I spy CDM

no, your stupid

August 19, 2006 at 9:28 pm | | wild web

I can how people get to this blog (anonymously—don’t worry whoever searched for this). I love this: recently, someone found this website by googling “how to tell if your stupid.” If you incorrectly spell “you’re” while asking how to tell if you’re stupid, you probably have your answer.

breaking the diffraction limit of light, part 1

August 19, 2006 at 8:52 pm | | literature, single molecules, tutorial

This is Part 1 in a (possibly) multi-part series on techinques that seek to image objects smaller than the diffraction limit of light. Part II is here. Suggestions for other interesting methods to summarize?

It is well known that there is a limit to which you can focus light—approximately half of the wavelength of the light you are using. But this is not a true barrier, because this diffraction limit is only true in the far-field and localization precision can be increased with many photons and careful analysis (although two objects still cannot be resolved); and like the sound barrier, the diffraction barrier is breakable! Let’s explore a few interesting approaches to imaging objects smaller than ~250 nm.

Probably the most conceptual way to break the diffraction barrier is to use a light source and/or a detector that is itself nanometer in scale. Diffraction as we know it is truly a far-field effect: the light from an aperture is the Fourier transform of the aperture in the far-field. [Here’s a neat Applet to play with.] But in the near-field, all of this isn’t necessarily the case. Near-field scanning optical microscopy (NSOM) forces light through the tiny tip of a pulled fiber—and the aperture can be on the order of tens of nanometers. If you bring this tip nanometers away from a molecule, the resolution is not limited by diffraction, but by the size of the tip aperture (because only that one molecule will see the light coming out of the tip). Then you can raster scan the tip over the surface to create an image.

The main down-side to NSOM is the limited number of photons you can force out a tiny tip, and the miniscule collection efficiency (if you are trying to collect fluorescence in the near-field).

Local Enhancement / ANSOM / Bowties
So what if, instead of forcing photons down a tiny tip, we could create a local bright spot in an otherwise diffraction-limited spot? That is the approach that ANSOM and other techniques take. ANSOM is apertureless NSOM: it uses a tip very close to a fluorophore to enhance the local electric field the fluorophore sees. Basically, the ANSOM tip is like a lightning rod which creates a hot spot of light.

The Moerner lab uses some bowtie nanoantennas to greatly and reproducably enhance the electric field in the nanometer gap between the tips two gold triangles. Again, the point is to enhance a very small region of a diffraction-limited spot, thus improving the mismatch between light and nanoscale objects—and breaking the diffraction barrier.

My most recent favorite is STED—stimulated emission depletion. Stefan Hell at the Max Planck Institute developed this method, which uses two laser pulses. The first pulse is a diffraction-limited spot that is tuned to the absorption wavelength, so excites any fluorophores in that region; an immediate second pulse is red-shifted to the emission wavelength and stimulates emission back to the ground state before, thus depeting the excited state of any fluorophores in this depletion pulse. The trick is that the depletion pulse goes through a phase modulator that makes the pulse illuminate the sample in the shape of a donut, so the outer part of the diffraction limited spot is depleted and the small center can still fluoresce. By saturating the depletion pulse, the center of the donut gets smaller and smaller until they can get resolution of tens of nanometers.


This technique also requires a rastor scan like NSOM and standard confocal.

Fitting the PSF
The methods above (and below) use experimental techniques to circumvent the diffraction barrier, but we could also use crafty analysis to increase our ability to know where a nanoscale object is. The image of a point source on a CCD is called a point spread function (PSF), which is limited by diffraction to be no less than approximately half the wavelength of the light. Of course. But what if we simply fit that PSF with a Gaussian to locate the center of the PSF—and thus the location of the fluorophore? Sure! But the precision by which we can locate the center depends on the number of photons we get (as well as the CCD pixel size and other factors). Regardless, groups like the Selvin lab and many others have employed this analysis to localize single fluorophores to a few nanometers! This, of course, requires careful measurements and collecting many photons.

What fitting a PSF is to localization, photo-activated localization microscopy (PALM) is to “resolution”—I use this term loosely to mean measuring the distance between objects, not true optical resolution. Eric Betzig and collegues developed PALM; Xiaowei Zhuang at Harvard used a similar techniques and calls it STORM: stochastic optical reconstruction microscopy. [UPDATE: Sam Hess at UMaine developed the technique simultaneously.] The basic premise of both techniques is to fill the imaging area with many dark fluorophores that can be photoactivated into a fluorescing state by a flash of light. Because photoactivation is stochasitic, you can ensure that only a few, well separated molecules “turn on,” then fit their PSFs to high precision (see above). If you wait until the few bright dots photobleach, then you can flash the photoactivating light again and fit the PSFs of different well spaced objects. If you repeat this process many times, you can build up an image molecule-by-molecule; and because the molecules were localized at different times, the “resolution” of the final image can be much higher than that limited by diffraction.


The problem? To get these beautiful pictures, it takes ~12 hours of data collection. This is certainly not the technique to study dynamics (fitting the PSF is better for that).

NSOM: 1,2
Enhancement: 1,2
STED: 1,2
Fitting PSF: 1

Combustible water

August 19, 2006 at 4:38 pm | | pseudoscience, stupid technology

This linked article was originally sent to the Stanford Electrocatalysis mailing list by Chris Chidsey.

The author, who claims to be a physicist, reports preliminary evidence on the formation of “HHO gas” by the electrolysis of water. The author claims that while this HHO gas is similar to a mixture of O2 and H2, it is in fact a different substance. The analyses are a joke (i. e. IR spectra of H2 and O2) and the interpretations are equally funny. The fact that this paper made it past the editor and through peer review is mind boggling. Can anyone seriously publish in the “International Journal of Hydrogen Energy” again?

Free samples of HHO gas (Aquygen) and instructions for its detection can be requested at From this website, you can watch the “inventor,” Danny Klein, brush his hand through the HHO flame to show that it is “safe” and does not burn the hand, and then miraculously cut through various materials (nevermind that he turns up the oxygen flow into the torch in between). Can this guy possibly believe that his HHO gas is real?

Schrodinger’s CATion

August 17, 2006 at 10:15 am | | crazy figure contest

I don’t think this illustration was taken from the original document, but seriously. While trying to illustrate the parity properties of singlet and triplet Cooper pairs, this illustrator decided the most appropriate representation for an electron was a cat (some reference to Alice in Wonderland.) Now we just need Pecora to scatter light off of it…


August 16, 2006 at 11:43 pm | | cool results

I’m just finishing up a class on Fourier transforms, and the discreet transform has me all gooey about sampling. Have you ever noticed that computer screens shown on TV sometimes have a line moving though the picture? It’s a sampling error. The frame rate of the TV camera is similar to the refresh rate of the computer screen. As a result, the refreshing sweep is visible. It’s like strobing a light with exactly the same frequency as a spinning fan. The result to your eye is a stationary fan. Check out the link in Figure 1.

Figure 1. Remember, this movie is shot and shown in real time.

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