self promotion

October 28, 2009 at 1:29 pm | | cool results, literature

But what is a blog for anyway? Advertising! Here’s my most recent paper:


“Azido Push−Pull Fluorogens Photoactivate to Produce Bright Fluorescent Labels” J. Phys. Chem. B

Sorry for the lame post, but I’ve been too busy to write cool things…

red laser pointers

October 13, 2009 at 3:42 pm | | conferences, nerd, science community

Open letter to presenters at Optical Society of America Meeting:

You are presenting at an optics meeting. It is unacceptable to use a cheap keychain red laser pointer. As a member of OSA, with a tag on your shirt that reads “LaserFest,” red laser pointers are embarrassing. (I suppose very bright red laser pointers are OK.)

Green pointers are best. Human eyes are highly sensitive in the green. At 630 nm, eyes are not nearly as sensitive.

Given that you’re at a lasers/optics conference, it is even cool to use a blue pointer—even though it is inefficient—just to demonstrate that you’re a stud.


photoactivation vs. photoswitching (part 2)

October 9, 2009 at 3:43 pm | | tutorial

In part 1, I discussed the differences between the definitions of photoactivation and photoswitching. Here, I want to talk about some of the applications of the various classes of photochromic dyes.


Photochromism typically is used for modulating the absorbance or color of a solution or material. The most obvious example is sunglasses that tint in the sunlight. Photochromism can even be applied to batteries!

Photoactivation is ideal for situations you want an emitter to start in a dark form, be controllably activated to a bright form, emit many photons, then disappear irreversibly. An example application is tracking single molecules when the concentration of molecules is high: you want the probes dark to start to maintain a low background, and you want the probe to turn on irreversibly lest the emitter switches off quickly and you can no longer track it.

Another perfect example is super-resolution imaging (via photoactivation and localization) of relatively static structures: you want to turn on a sparse subset of emitters, localize them once with high precision (requires many photons), then have them disappear permanently. Using a photoswitching probe for imaging static structures isn’t ideal, because relocalizing the same spot over and over wastes time and complicates the subsequent image analysis.

Photoswitching is ideal if you want to relocalize over and over, such as if you are performing super-resolution imaging on a moving or dynamic structure. Photoswitching can also be applied to speckle microscopy, which follows fluctuations in dynamic filaments. Others have used photoswitching to modulate a probe, lock-in to that modulating signal, and filter out the unmodulated background from nonswitching fluorophores (see OLID, figure below).


Photoswitching is also necessary for super-resolution techniques such as STED and structured-illumination, which require many cycles of bright and dark. In fact, both these techniques require photoswitching that is very robust and lasts many many cycles.

Side Note Regarding Photons: It is important to note that a compound being switchable does not necessarily mean that it will ultimately emit more photons. In many cases, cycling emission simply spreads the photons into many bins: the total number of photons emitted over all the cycles sum up to the same number to the situation if the fluorophore had been on continuously. For instance, if the unswitching form of the fluorophore usually emits about a million photons (for the best organic dyes), then you cycle it with each cycle emitting 10,000 photons, the photoswitch will generally last 100 cycles on average before photobleaching.

On the other hand, it is conceivable that a photoswitch could resist photobleaching better than its continuous analog. For instance, if the fluorophore bleaches via producing triplet oxygen that builds up around the dye—eventually colliding and reacting with the compound—then switching to an off state might offer some time for the built up concentration of triplet oxygen to dissipate.

On the third hand, if the switch is capable of bleaching from the dark state, then switching may ultimate reduce the total photon count (e.g. the imaging light may pump the dark form into highly excited triplet or other states, leading the compound to basically explode).

ribosomes are cool

October 7, 2009 at 1:19 pm | | science and the public, science community

There’s a lot of complaining on the chem blogosphere and in chemistry departments around the world about this year’s Nobel Prize in Chemistry. What? Going to biologist again!?!?

Personally, I don’t find this year’s chemistry prize at all offensive. We chemists love to tout chemistry as the nexus of all fields of science, from physics to biology. So we shouldn’t be too upset when researchers outside our personal subfield wins a chemistry prize.

Moreover, the chemistry Prize has always been awarded a range of experiments. (Think nuclear physics in the early part of the 20th century.) Biology is today a maturing field with amazing breakthroughs daily, so it’s not surprising that biological chemistry wins prizes.

And ribosomes are very cool.

what do CCDs and optical fibers have in common?

October 6, 2009 at 8:57 am | | history, science and the public, science community

Answer: they’re both super important. (And they both won this year’s Nobel Prize in Physics.)

Upon hearing this prize announcement, just about everyone I know thought, Yup, those are important. Some people also thought, Why are they sharing the same prize? And at least one person thought, How did they shoot live video before the CCD?

They used basically a reverse television, the pickup tube:


Get it?

Powered by WordPress, Theme Based on "Pool" by Borja Fernandez
Entries and comments feeds. Valid XHTML and CSS.