volcanoes are your solution to everything

September 30, 2009 at 5:04 pm | | science community, seminars, stupid technology

After John Deutch‘s talk this afternoon, one student asked three (!) questions. His third one was: “Why don’t we just take nuclear waste, seal it in some container, then put it at the bottom of the Mariana trench. That way, it would get sucked up into the center of the Earth and not be a problem.”

I’m serious. That was his question … his third question.

Deutch’s response was: “It’s probably not best if each person comes up with their own technological solutions to the energy problems.”

There needs to be a one-question-per-first-year rule.

sorry IE users

September 25, 2009 at 4:57 pm | | wild web

Sorry to the 20% of folks who visit my site using Internet Explorer. I just noticed that the site is basically broken using that browser. Oops.

Unfortunately, I’m too lazy to fix it. Sorry.

The site does work with Firefox, Safari, Chrome, Opera, Camino, Netscape, Opera Mini….

AC now has letters

September 22, 2009 at 9:13 am | | literature, science community

Anal. Chem. has begun accepting shorter publications as letters. I think that’s probably a good idea: another option when publishing a short, timely, interesting result.

Ubiquitous oxymoron in journal articles and the English vernacular

September 20, 2009 at 12:03 am | | help me, nerd

How many times have you heard someone refer to the “biggest bottleneck” in some process? I’d guess at least once a week if you’re an engineer. Now think about that for a moment.  Biggest bottleneck?  Exactly how much flow does a BIG bottleneck suppress? I didn’t have this epiphany until I typed “smallest bottleneck” in my dissertation.  But “biggest bottleneck” wins over “smallest bottleneck” by an 84:1 margin according to Google.  It is not rigorously an oxymoron, however, because there could literally be a series of bottlenecks and one could be the biggest (i.e., largest bore diameter), but the manner in which the term is commonly used suggests a contradictory role between the adjective and noun. I guess it’s like people saying “I could care less” when they mean “I couldn’t care less.” Am I crazy or does this bother anyone else?  “Accuracy above all else,” I say.

epi tube as a lava lamp

September 18, 2009 at 7:51 am | | crazy figure contest, literature

Nice, a lava lamp in table-of-contents artwork.


Oh, wait. That’s an epi tube.

2009 EDSEL-Nobels

September 16, 2009 at 9:27 am | | EDSELs, science community

edsel_nobelTime for the 2009 EDSEL-Nobels. Just to clarify, these are not predictions for the real Nobel. Instead, they are relatively arbitrary awards given to great scientists.

This year’s criteria include: how many papers/books I’ve read from the scientists, whether I’ve seen them give a talk, and how they’ve contributed to a field I am interested in.

The 2009 EDSEL-Nobel Prizes go to Nicholas J. Turro (Columbia) and Josef Michl (Colorado) for their research and literary contributions to photochemistry.

I have used both their books (here and here) extensively in my own research. I had the pleasure of seeing an interesting talk by Turro last year and look forward to seeing Michl in a couple weeks at Stanford’s Johnson Symposium.

protect the non-born-oppenheimer!

September 9, 2009 at 12:49 pm | | crazy figure contest, literature, wild web

This is how the table-of-contents artwork showed up in my RSS reader:


Oops. It turns out that the artwork was supposed to look like this:


It takes some balls to make your TOC “artwork” a big, complicated equation.

how not to choose a title 101

September 8, 2009 at 3:12 am | | great finds, literature

It’s easy for one to find amusement in a poorly conceived figure or in a t-shirt attempting to show the structure of PCP but failing quite miserably or in the egregious cover of an Oxford University Press promotional booklet for ACS publications. But let us not overlook the gems of humor that we encounter everyday in the form of journal-article titles. Throughout the process of writing my dissertation, I have accumulated countless EndNote libraries, the entries of which are fertile grounds for laughter. I challenge you to improve upon these categories (or add new ones):

Greatest disregard for the importance of being concise:

Bennett, M. A.; Yoshida, T. J. Am. Chem. Soc. 1978, 100, 1750-1759.

long title
Most dizzying:

Arroyo, M.; Bernès, S.; Brianso, J. L.; Mayoral, E.; Richards, R. L.; Rius, J.; Torrens, H. J. Organomet. Chem. 2000, 599, 170–177.

Most [{(=flamboyant=)}]:

López, O.; Crespo, M.; Font-Bardía, M.; Solans, X. Organometallics 1997, 16, 1233-1240.

Most clichéd:
Gaydos, C. A. Neurology 2001, 56, 1126-1127.


Longest running series (most pretentious?):
ten Brink, G.-J.; Arends, I. W. C. E.; Hoogenraad, M.; Verspui, G.; Sheldon, R. A. Adv. Synth. Catal.
2003, 345, 1341-1352.

longest series
Most in need of an editor (and a vacuum pump to remove those 0.88 +/- 0.04 molecules of methylene chloride):

Usón, R.; Forniés, J.; Espinet, P.; Garcia, A.; Tomas, M.; Foces-Foces, M.; Cano, F. H. J. Organomet. Chem. 1985, 282, C35-C38.

I still have four chapters of my dissertation to write and only four days before a draft is due to my committee.  I can’t help but to ask myself, Is this the best use of my time?

photoactivation vs. photoswitching (part 1)

September 3, 2009 at 10:18 am | | tutorial

With the development of new super-resolution imaging techniques, photoswitching probes have become very important. Here, I explain the differences in photophysics and applications of photoactivating and photoswitching fluorophores. (These are not hard-and-fast rules, just my definitions of the terms.)


In general, photochromism refers to the reversable light-induced transformation of a compound between two forms that absorb different energies or amounts of light. By switching between the forms, the color of a solution of the chromophore changes. One or both forms may be fluorescent, but it is possible that neither form fluoresces significantly. Frisbees or beads or shirts that change color in sunlight probably contain some photochromic molecules that are switched using UV irradiation. Common photochromic compounds include azobenzenes (structure above), diarylethenes, and spyropyrans.

Photoswitching refers to the reversable light-induced switching of fluorescence (color or intensity), and is often a type of photochromism. (In general, there is really no reason that the term must refer only to fluorescence, but in the context of imaging it is more helpful.) For instance, photoswitching rhodamines cycle between nonfluorescent and fluorescent forms by closing and opening a lactam ring. When the ring is closed (the thermally stable form), the absorbance is in the UV and the compound is nonfluorescent. Upon irradiation with UV light, the lactam can open; this forms a metastable fluorescent compound that absorbs in the green. Eventually, the lactam ring reforms (either via visible-light irradiation or thermally), and the cycle can repeat. Eventually, some photochemical reaction with change the compound (e.g. photo-oxidation), and the cycling will end (see cycling below). This is called photobleaching. Another example of cycling photoswitching includes Cy5 (here and here), which can be attacked by a thiol and rendered nonfluorescent; by irradiating with green light, the thiol pops back off and the Cy5 becomes fluorescent again. Here is a plot of the cycling fluorescence of Cy5:


Photoactivation refers to the irreversable light-induced conversion of a fluorophore from a dark form to a fluorescent form (or from one emission color to a significantly shifted color, e.g. blue to red). Typically, a chemical reaction transforms the compound, thus making the photoactivation irreversable for all practical purposes. For this reason, a photoactivatable fluorophore is sometimes referred to as being photocaged. There are several photoactivatable fluorescent proteins, such as PA-GFP. Another example close to my heart is the azido DCDHF fluorophore: upon irradiation with blue light, an azide photoreacts into an amine (with the loss of N2) and converts a nonfluorescnt compound to a bright emitter.


In the next installment (part 2), I will describe the situations where photoswitching is preferred over photoactivation and vice versa.

energy flow charts

September 2, 2009 at 12:12 pm | | science and the public

Here are some cool energy flow charts:


(source: LLNL and Whitesides review)


(source: GCEP)

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