Good Conduct

August 15, 2006 at 5:47 pm | | everyday science, hardware

My lab is involved in several highly sensitive experiments that require complex data acquisition hardware. Much of our hardware is homemade, old, or inevitably unstable. As a result, we have to spend time fixing these systems, and that cuts into actual experiment time. To streamline the repair work and prevent future breakdowns, we have developed the flow chart shown in Figure 1.

Figure 1. Dishearteningly accurate.

I really like this figure. It’s truly a contender for best figure ever.

measuring total photons emitted

August 15, 2006 at 10:09 am | | everyday science, single molecules, tutorial

Good single-molecule fluorophores must meet several criteria. To name a few, the molecules must have high quantum yields, must be photostable, with a large absorption cross-section and a low yields into dark triplet states. (Ideally, a single-molecule fluorophore would have some inherent reporter function, but that’s a story for another day.) There are several popular long-lasting, bright fluorophores out there (e.g. rhodamines, terylenes, Cy3); my research involves developing and characterizing new compounds for single-molecule cellular imaging, which means quantifying the criteria I listed above.

One measure of photostability is the total number of photons each molecule emits before it irreversibly photobleaches (Ntot,emitted). Because photobleaching is a Poisson process that depends on the number of times the molecule reaches the excited state, Ntot,emitted for a fluorophore should not depend on the laser intensity (unless you illuminate beyond the saturation intensity): at a higher intensity, the molecules will absorb and emit photons at a higher rate, but photobleach in less time, yielding the same number of photons than at a lower intensity. So the Ntot,emitted of a particular fluorophore in a particular environment tells you how bright or long-lasting the fluorophore is; the higher the number, the better the fluorophore (all else the same).

I’ve measured the Ntot,emitted for a fluorophore on the bulk and single-molecule level—experiments which require different analysis. For the single-molecule measurement, I record movies of a wide-field illumination of several molecules well spaced in a polymer film. Then I integrate the counts from each molecule and plot the distribution from over 100 individual molecules. The distributions look like this:


The distributions are exponential characteristic of a Poisson process. From this distribution, I can determine the average Ntot,detected and convert this to Ntot,emitted using the detection efficiency of my setup (typically ~10% for epifluorescence).

The bulk measurement is a little less conceptually obvious. I use the same setup, but overdope the dye into the polymer film, so the intensity of the entire field of view versus time in the movie looks like this:


From the exponential fit, you can extract the average time before photobleaching for the molecules. This value, combined with the absorption cross section and the laser intensity, can give you the number of photons absorbed per molecule. Using the quantum yield, you can then calculate the Ntot,emitted.

So what’s my whole point here? Given that the two experiments I describe use different measurements and calculate Ntot,emitted using different parameters, I was really happy to see that the calculated values of Ntot,emitted were very close from bulk and single-molecule experiments when I compared them directly. That’s all.

[Update: You can find some of the relevant equations in this paper or the SI of this paper.]

write-your-own caption!

August 14, 2006 at 7:37 am | | crazy figure contest, literature

From an article, Image scoring and cooperation in a cleaner fish mutualism, in Nature:


Whoever comes up with the best caption for this silly figure will win an EDS refrigerator magnet.

Wiktionary, I’ve got a word for you

August 11, 2006 at 11:37 am | | wild web

I’m a big fan of wiki. But, I just ran across, and I don’t like it.

Wikipedia makes sense. A bunch of people compiling ideas and information. But, compiling word definitions sounds silly when you consider the already available resources and the mistakes people will certainly make.

Oh snap, time for the burrito truck.

reading babies’ minds

August 7, 2006 at 10:35 pm | | crazy figure contest, literature

This PNAS paper just freaked me out: Baby with wires coming out of the brain!


If that’s not a “Worst Figure,” then what is?

The point of the paper was to test the theory that extended staring means that the baby didn’t anticipate what it saw, a common method used to test the world view of babies and monkeys. But I didn’t actually read the paper, because the figure scared me too much.

Thanks, Andrew, for bringing this paper to my attention. Thanks also for the nightmares. Very H.R. Geiger.

RC humans

August 7, 2006 at 5:47 pm | | news, stupid technology

This sounds really fun. I wanna get myself an RC human. I would make him go do my laundry.

The real proof that this is a useful technology will be when they can remotely control a human to control an RC car. That will be true progress.


obscure patents

August 4, 2006 at 11:01 am | | nerd, stupid technology, wild web

Here’s a nice website collecting obscure patents. Very helpful to stimulate those creative juices.

Stereotypes are Real

August 4, 2006 at 8:39 am | | nerd

My alma mater did well in the National Quiz Bowl Tournament this year with a 6th place finish. We beat Harvard for the win back in ’79, and that was when the game was pure and winning really mattered. Our victorious team is featured in Figure 1.

Figure 1. Winners.

There are no barbers in Davidson, North Carolina.

a better atomic clock

August 3, 2006 at 3:57 pm | | literature

Researchers from NIST in Bolder, CO have produced a high-precision clock using a single Hg atom, which they claim out-precisions the standard Cs clock which we currently use to define the second. They use a UV laser (as opposed to the microwave laser used for the Cs clock) to excite the atom, which means that the frequency can be known with greater precison. The frequency of the UV transition was measured to be 1,064,721,609,899,144.64 Hz—oops, I wrote that wrong, it’s actually 1,064,721,609,899,144.94 Hz.

According to Nature, “the clock is expected to drift by only 1 second in 400 million years compared with 1 in 60 million in caesium clocks.” Well thank god.


August 1, 2006 at 4:37 pm | | everyday science, hardware

Our 12 W Ar ion laser needed a tube change.* All it took was three weeks to convince Spectra Physics and two days with the service engineer. In the end, she’s a beaut’, Clark (see Figure 1).


Figure 1. Looking good, Billy Ray. Feeling good, Louis.

*The tube is changed every 6-12 months.

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