dissertation acknowledgments

March 19, 2015 at 2:27 pm | | everyday science, grad life, history

Paul and ChemJobber posted about acknowledgements in theses and dissertations. Paul has a nice one here. It made me reread mine:

Acknowledgements

Most importantly, I thank my advisor, W.E. Moerner. It is difficult to explain how wonderful it has been to study under him. W.E. is a real scientist’s scientist: he fundamentally cares about good science and presenting results in a clear and honest manner. He always impressed me with his understanding of sciences outside his field and his scholarship, as I doubt that there is any paper I have read that he has not. W.E. always knows where some obscure piece of equipment is in the lab, and what type of power cable it requires. W.E.’s humor and generosity have been invaluable during my time in his lab, not to mention his scientific guidance. I could not have asked for a better Ph.D. advisor.

I joined the Moerner lab because W.E. seemed to run a fun and exciting research program, and I have not been disappointed. Other members of the Moerner Lab have been instrumental in my education and research. Kallie Willets mentored me when I first arrived at Stanford. Kallie was fun to work with and I am very grateful for the time and energy she dedicated to helping me get a solid footing in the lab by teaching me the right way to do things (and clean up afterwards).

After Kallie graduated, it was entertaining (to say the least) to get to know my officemate Dave Fromm. Dave was always willing to discuss problems I was facing in my experiments, and often suggested perfect solutions. (He was also always willing to discuss his adventures and funny stuff he found on the internet.) Dave and Jim Schuck regularly played darts over my head … literally. In general, this was entertaining and helpful to my overall spirit, and I appreciate the fun times with Jim and Dave. In those early years, I also enjoyed the company of (and scientific input from) Nick Conley, Anika Kinkhabwala, Adam Cohen, Stefanie Nishimura, Jaesuk Hwang, Kit Werley, So Yeon Kim, Andrea Kurtz, Marcelle Koenig, and Jian Cui.

In the later years of my tenure in the Moerner Lab, I have benefited from another batch of amazing people. Nick is one of the most motivating collaborators I have had the pleasure of working with; he is always excited about results, and his mind wanders to great places (not to mention that his skills as an organic chemist were very helpful to me)! I also had the opportunity to work with Hsiao-lu Lee, who was always generous with her time and expertise in cell culture. I am thankful to have those two wonderful coauthors. Alex Fürstenberg has been a fun (and very tolerant) officemate, and is always a great person to ask about anything photophysical. Mike Thompson is hard working and smart, but most importantly he laughs at more than 83% of my jokes. Julie Biteen is opinionated and usually right, and has been fun to bounce ideas off. All the other members of the Moerner Lab (Shigeki, Randy, Majid, Steve, Jianwei, Whitney, Lana, Yan, Sam B, Quan, Matt, etc.) are exceptional people and have made Stanford a wonderful place.

Marissa Lee started joined the lab in 2008, joining my project. I have enjoyed mentoring her and passing on as much as possible of what Kallie, Dave, Jim, Stefanie, Nick, Hsiao-lu, So Yeon, Jaesuk, Adam, and Anika taught me over the years. I wish her luck in her time at Stanford. Several summer students worked with me to get a taste of research. I thank Jennifer Alyono, Daniel Lau, Nathan Hobbs, and John Servanda for their help taking spectra.

Of course, I must also acknowledge Bob Twieg and his students at Kent State University. As a physical chemist, there is nothing better than an excellent collaboration with a group of top-notch synthetic chemists. W.E. and Bob have worked together since their IBM days in the 1980s and 1990s, and I had the fortune to benefit immensely from that bond between labs. Nearly every compound mentioned in this Dissertation was synthesized by the Twieg lab, and the back-and-forth (or push– pull?) design process between the labs should serve as an example to what all collaborations should strive for. Bob’s students have made great compounds over the years, and I thank all of them for being super collaborators: Meng, Hui, Zhikuan, Na, Reichel, Ryan, Alex, and Jarrod.

Friends have made grad school a blast. I met the Moilanens immediately, and enjoyed marathon training and adventures with David and Hailey. Ben Spry was a great help studying for placement exams, and I enjoyed driving to San Jose with Ben so he could buy a Camaro. William Childs and Charles McCrory—after I finally decided to like them—were indispensible: grad school will be filled with fond memories of coffee, lunch, and arguments because of Wm and Charles. So many other friends made my time at Stanford wonderful: Nichole, Kate, Alicia, Jen, Drew, Ashley, John, Zalatan, Chad, Matt, Griffin, Kendall, Daniel, Adrienne, Adam, Avisek, Eric, Ethan, Kevin, Emily, Ken, Dan, Scott, and everyone else! It has been fun having Jordan and Maria in California, and so many other non-Stanford friends that I cannot possibly name them all. I have had positive interactions with several faculty members, and I thank Bob Waymouth, Chris Chidsey, Dick Zare, Bianxiao Cui, Steve Boxer, Justin DuBois, Vijay Pande, Bob Pecora, and Ed Solomon. I also must recognize the members of the Stanford staff who contributed to my work and enjoyment, namely: Roger Kuhn, Todd Eberspacher, Brian Palermo, Patricia Dwyer, Grace Baysinger, Steve Lynch, and all the Conways—Marc, Daragh, and Mariette.

I feel that I must also acknowledge those in my past who influenced me and led me down the path of science. My earliest memories of enjoying the natural world were at Audubon’s Mast Landing Camp, playing and learning about nature with Aaron and Ira and Matt. In the third grade, Mrs. Solari recognized and encouraged my inclination toward science, as have many teachers since. I thank Dr. Root, who mentored me for my 7th-grade science fair project; Mr. Plummer for dealing with 8th graders; Mr. Glick for the astronomy and recycling clubs and supporting me throughout high school; Mr. Herrick, for being the best physics teacher I never had; Mr. Gauger for insisting that Heisenberg’s uncertainty principle can explain why things still jiggle at zero Kelvin; John Anderson for arguing with me; Don Cass for teaching my first college chemistry class and making it so exciting; Tony Planchart for teaching biochemistry in a way that convinced me to be a chemistry major; Helen Hess for fun classes biology and biomechanics; Michael Rubinstein for his entertaining exploration of polymer physics; Royce Murray for teaching analytical chemistry; Max Berkowitz for stat mech classes; and Charles Schroeder, Eric Shaqfeh, and Steve Chu for a great summer research experience. I should offer a special bit of gratitude to Sergei Sheiko, whose lab I worked in as an undergrad, and who helped make my time at UNC spectacular.

This Dissertation is dedicated to my family: the Lords, the Cyrs, and the Hearns. My parents have always encouraged my interests, without pushing me too hard. I wouldn’t be half the person I am without their support. My brother Jackson has been a life-long companion, so I was very pleased when he moved to California and we could play together like when we were growing up. My grandparents Lord funded my education, which I greatly appreciate. I probably get some of my curiosity from my pépère Cyr. My first year at Stanford, I met Brenna Hearn and married her a few years later. She has made my life wonderful, and I thank her for her support throughout grad school. I cannot thank Brenna enough for her companionship, so I’ll stop there.

Looking back at this, I wish that I had made it 50 times longer and cut out the rest of the dissertation.

2014 Nobel roundup

October 8, 2014 at 11:06 am | | history, news, nobel

W.E. Moerner is really the father of single-molecule spectroscopy. It’s not surprising that a prize for single molecules went to him. His early work laid the foundation for single-molecule photophysics that made PALM-type super-resolution possible.

Also, most people don’t realize that almost all the early cryogenic single-molecule imaging resolved molecules that were closer than the diffraction limit. At temperatures near absolute zero, the spectral linewidths get super narrow. This means that any one laser wavelength excites only a fraction of the dyes in a crystal; dyes in different parts of the solid experience slightly different nano environments, and their spectral properties are different. This is called inhomogeneous broadening. By tuning the wavelength of a dye laser, Moerner and others were able to excite different dyes at different times, all within one diffraction-limited laser spot. That was routinely done, and many of the early single-molecule images were actually plots of intensity, with distance on one axis (moving the laser spot) and wavelength on the other (changing the laser color).

broadening

Fluorescence excitation spectra for pentacene in p-terphenyl at 1.5 K measured with a tunable dye laser of line width ∼3 MHz. The laser detuning frequency is referenced to the line center at 592.321 nm. (a) Broad scan of the inhomogeneously broadened line; all the sharp features are repeatable structure. (b) Expansion of 2 GHz spectral range showing several single molecules. (c) Low-power scan of a single molecule at 592.407 nm showing the lifetime-limited width of 7.8 MHz and a Lorentzian fit. [From: Moerner, W. E. J. Phys. Chem. B 2002, 106, 910– 927.]

 

 

sms2

[From: Ambrose, W. P. and Moerner, W. E. Nature 1991, 349, 225– 227]

Eric Betzig contributed to single-molecule spectroscopy early on, imaging single molecules at room temperature with near-field super-resolution microscopy (Betzig 1993) and proposing an early variant of PALM super-resolution imaging back in the 1990s (Betzig 1995). (His proposal was realized at cryogenic temperatures by van Oijen in 1998.) After that, he left science and worked at his father’s tool factory.

When Betzig heard about the development of GFPs that could be easily photoswitched on and off, he realized that these could be applied to his super-resolution concept he proposed a decade earlier (Betzig 1995). So he built a super-resolution microscope in his friend’s living room and published the first PALM paper in 2006. It should be noted that Xiaowei Zhuang and Sam Hess each independently published similar super-resolution methods in 2006 (Betzig 2006; Hess 2006; Rust 2006).

betzig early palm

 

[From: Betzig 1995]

Stefan Hell has a very interesting story. After proposing STED microscopy in the 1990s (Hell 1994), he worked for years with little funding and almost no support or recognition. A decade later he got his STED microscope producing super-resolution images and now he’s a huge force in the field.

It goes without saying that there were many others who contributed to the field of super-resolution and single-molecule imaging (Yanagida, Webb, Zhuang, Hess, Gustafsson, Lippincott-Schwartz, Zare, Vale, Orrit, Rigler, Xie, Cremer, Baer…) and many people will probably be disappointed. But is hard to argue that these three were not deserving and I congratulate them!

Also, Ash at Curious Wavefunction has a great summary. See my post from 2006 on super-resolution methods. And my single-molecule timeline (please excuse any omissions: it is impossible to include everyone!). And remember when the Simpsons predicted W.E. to win?

And full disclosure: W.E. was my PhD advisor. :)


Ambrose, W. P. and Moerner, W. E. Nature 1991, 349, 225– 227.

Betzig E and Chichester RJ (1993) Single molecules observed by near-field scanning optical microscopy. Science 262:1422-1425.

Betzig E (1995) Proposed method for molecular optical imaging. Opt Lett. 20:237-239.

Hell SW and Wichman J (1994) Breaking the diffraction resolution limit by stimulated emission: stimulated-emission-depletion-microscopy. Opt. Lett. 19:780-782.

Hess, S. T., Girirajan, T. P. K. and Mason, M. D. Biophys. J. 2006, 91, 4258–4272

Rust, M. J., Bates, M. and Zhuang, X. Nat. Methods 2006, 3, 793– 795

van Oijen AM, Kohler J, Schmidt J, Muller M and Brakenhoff GJ (1998) 3-Dimensional super-resolution by spectrally selective imaging. Chem. Phys. Lett. 292:183–187.

speck of dust

April 18, 2014 at 10:43 am | | crazy figure contest, history, literature

The scope room dustiness post reminded me of the hilarious story of the first report of second harmonic generation (SHG) of a laser. The authors presented a photographic plate that showed the exposure the main laser beam, as well as a “small but dense” spot from the doubled beam,

shg dust

See the spot? You won’t. Because the editor removed the spot, thinking it was a speck of dust on the plate. Ha!

When I first heard this story, I didn’t believe it. I assumed it was a contrast issue when the paper was scanned into a PDF. So I went to the library and found the original print version. No spot there, either!

That really made my day.

c&e news archive

November 9, 2010 at 10:10 am | | history, literature

Well, Paul inspired me to go check out the C&E News Archives. I looked for some p-chemists at my (PhD) alma mater. I was happy to find an article about my PhD advisor, W.E. Moerner:

The best one I found was on Steve Boxer, mostly because of the photo and caption:

And several articles on Zare, like this one.

History is fun.

UPDATE: A quaint story about a growing department at Stanford.

Also, a cool pic of my old building, from 1961! That building still has those same windows.

crick’s lost letters

October 1, 2010 at 7:05 am | | history, news, science community

Some revealing letters of Francis Crick have been found—mostly to Maurice Wilkins—and they discuss Rosalind Franklin. Here are some of the excerpts that I found interesting. For instance, this letter from Wilkins to Watson and Crick after they proposed the double-helix model:

My dear Francis,

I gather you have got the coordinates of your model or some worked out. Do you think we could have a copy of what you have?

The crystalline data is clearing up nicely. To think that Rosie had all the 3D data for 9 months & wouldn’t fit a helix to it and there was I taking her word for it that the data was anti-helical. Christ.

We have redone a lot of the 3D more accurately on mouse & will need all the extra accuracy for dealing with some of the finer points.

Regards & to Odile too.

Yours

M

P.S. I think I have a flat.

But “Rosie” had been focusing on the A structure of DNA, which generated clearer crystal diffraction pattern images. Unfortunately for her, crystalline DNA-A wasn’t helical. Crick agreed when he eventually saw her data:

This is the first time I have had an opportunity for a detailed study of the picture of Structure A, and I must say I am glad I didn’t see it earlier, as it would have worried me considerably.

All in all, it sounds like Franklin was generally unfriendly to her colleagues (and competitors). Wilkins wrote to Crick of Franlkin’s leaving King’s College:

I hope the smoke of witchcraft will soon be getting out of our eyes.

It sounds like her colleagues didn’t like her too much. But there was friction from the beginning: Wilkins thought that Franklin was going to work for him … or at least they would work together on DNA … and Franklin had been told that she would work independently. What a mess.

I feel bad for Franklin having to deal with these sexist jerks. Watson and Crick were probably the most annoying, because they didn’t do any experiments; instead, they’d listen to Franklin (and others) present their data, then run off and make a model. Annoying. Intellectual thievery almost. (And Watson and Crick admit as much, referring to it as “burglary” in one of their letters.)

But on the other hand, it seems Franklin made some serious mistakes interpreting her data and was quite abrasive. No angels here. No devils (or witches?) either.

I suspect that if everyone had worked together and been friendly, Watson and Crick would have proposed the correct structure much earlier. Not only that, but I think Franklin would have been given more credit by the boys. But that’s just my speculation. I just know that I’d prefer to collaborate with folks than fight with them.

academic genealogy

July 13, 2010 at 11:02 am | | history, science community

Jeremy over at Chemistryblog posted a few sites with info on academic lineage of many chemists. That inspired me to finish researching my academic genealogy. Kallie’s page at UT’s site was a nice confirmation of the lineage I had independently found. But I actually found links further back (through Rowland to Helmholtz, and eventually back to Leibniz’s dad); I’m not exactly sure why the UT page stops at Mendenhall.

I also explored my lineages from my undergrad and postdoc advisors. Interestingly, those two lines meet up in the mid-1800s (Liebig).

Anyway, below is the entire tree.

(I know this is a little self-indulgent. But whatever.)

Sam’s Academic Genealogy (via PhD advisor)

Samuel Joseph Lord
Postdoctoral research 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

William Esco Moerner (Stanford)
PhD Cornell 1982 (under A.J. Sievers)
BS Washington University 1975

Albert John Sievers III (Cornell)
PhD Berkeley 1962 (under Michael Tinkham)
BA Berkeley 1958

Michael Tinkham (Berkeley, later Harvard)
PhD MIT 1954 (under M. W. P. Strandberg)
BA Ripon College

Malcom Woodrow Pershing Strandberg (MIT)
PhD MIT 1948 (under A.G. Hill)
BS Harvard 1941

Albert Gordon Hill (MIT)
PhD Rochester 1937 (under Lee Alvin DuBridge)

Lee Alvin DuBridge (Rochester)
PhD University of Wisconsin–Madison 1926 (under Charles Elwood Mendenhall)

Charles Elwood Mendenhall (Wisconsin)
PhD Johns Hopkins 1898 (under Henry Rowland)

Henry Augustus Rowland (Johns Hopkins)
Civil Engineering degree Rensselaer Polytechnic Institute 1870
later studied under Helmholtz in Berlin

Hermann von Helmholtz (Berlin)
PhD Royal Friedrich-Wilhelm Institute (under Johannes Peter Müller)

Johannes Peter Müller
Bonn University (under Philipp Franz von Walther & Karl Rudolphi)

Karl Rudolphi … Friedrich Leibniz (1597-1652) [Gottfried Wilhelm Leibniz’s father]
Philipp Franz von Walther … Gerard van Swieten (1700-1772)

Sam’s Academic Genealogy (via postdoc advisor)

Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

Jay T. Groves (Berkeley)
PhD Stanford 1998 (under Steve Boxer)
BS Tufts 1992

Steven G. Boxer (Stanford)
PhD Chicago 1976 (under Gerhard L. Closs)
BS Tufts 1969

Gerhard L. Closs
PhD Tübingen 1955 (under Georg Friedrich Karl Wittig)

Georg Friedrich Karl Wittig
PhD Marburg 1923 (under Karl Friedrich von Auwers)

Karl Friedrich von Auwers
Berlin, 1885

August W. von Hofmann
Giessen, 1841

Justus von Liebig
Erlangen, 1822

. . .

Niccolò Leoniceno (1428-1524)

Sam’s Academic Genealogy (via undergraduate advisor)

Samuel Joseph Lord
Postdoctoral research Berkeley 2010- (under Jay T. Groves)
PhD Stanford 2010 (under W.E. Moerner)
BS University of North Carolina at Chapel Hill 2004 (under Sergei S. Sheiko)

Sergei S. Sheiko (UNC)
Habilitation University of Ulm 2000 (under Martin Möller)
PhD Institute of Chemical Physics of the Russian Academy of Sciences 1990
MS Moscow Physico-Technical Institute 1986

Martin Möller (Ulm)
Postdoctoral research University of Massachusetts (under Robert W. Lenz)
PhD University of Freiburg 1981 (under Hans-Joachim Cantow)

Hans-Joachim Cantow (Freiburg)
PhD University of Mainz 1950 (under G.V. Schulz)

Gunter Victor Schulz (Mainz)
PhD Kaiser Wilhelm Institute of Physical Chemistry and Electrochemistry 1932 (under Herbert Freundlich)

Herbert Freundlich (Kaiser Wilhelm Institute)
PhD University Leipzig 1903 (under Wilhelm Ostwald)

Wilhelm Ostwald (Leipzig)
PhD 1878 Dorpat University (under Carl Schmidt)

Carl Schmidt (Dorpat)
PhD University of Giessen 1844 (under Justus von Liebig)

Justus von Liebig
Erlangen, 1822

. . .

Niccolò Leoniceno (1428-1524)

to be unpublished

December 23, 2009 at 11:53 am | | history, literature

Footnote 20 is great.

Lipscomb, W. N. J. Chem. Phys. 1954, 22, 985-988. (Thanks Mike.)

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:

pickup-tube-wiki

Get it?

1966

May 21, 2009 at 8:59 am | | history, literature, science community

I guess I was the first one to check out this book since 1966.

1966-book

It wasn’t worth checking out, by the way.

khemistry klassics

December 5, 2008 at 3:49 pm | | great finds, history, open thread, science community

I want to start collecting the great (humorous) chemistry papers. Below are some that I can think of. Please comment with more!

  • One of the best quotes in a chemistry paper is the following: “This work will be continued and I wish to reserve the field for myself.” (Gomberg, M. An Instance of Trivalent Carbon: TriphenylmethylJ. Am. Chem. Soc. 190022(11), 757–771.)
  • A good April-fool’s article is Dick Zare’s (Wayne Knox’s) zero-fs pulse. (Knox, Knox, Hoose, Zare. Observation of the 0-fs pulse. Optics and Photonics News, April 1990.) This one also has a great quote at the end: “We are investigating possible violations of thermodynamics. Somebody’s pulses must be getting longer.”
  • The Alpher, Bethe, Gamow paper has it’s own Wikipedia entry! (Alpher, Bethe, Gammow. The Origin of Chemical ElementsPhysical Review, 1948, 73(7), 803-804.) Gammow, a jokester, added Bethe without his knowledge in order to have the names sound like the first three Greek letters. I guess Alpher—the grad student on the paper—was very reluctant to add Bethe, and has always worried that it took away some of his credit. Bethe did see the paper before it was published.
  • This is a new “classic,” but the TOC art really got a lot of internet press. (Toma, et al. Inorg. Chem. 200443, 3521-3527.) Was it intentional? Also funny: the TOC image is missing from ACS right now!

  • I really want to find that paper with the man fishing in the glassware. Anyone remember the citation?

Anyway, please let me know if you think any other papers should be included in this humorous group.

attila szabo’s autobiography

August 30, 2008 at 6:37 pm | | grad life, history, literature, nerd, science community

If you want a fun and inspiring story, read Attila Szabo‘s autobiography for his JPCB Festschrift (here). It’s only 4 pages.

Here’s a great except:

How could I get my hands on a little red phosphorus? Who would sell some to a 14 year old boy? Well, Fisher Scientific would.

Enjoy!

Happy L.A.S.E.R. Day!

May 16, 2008 at 9:57 am | | history, news

When I hit the google front page, I almost leaped for joy.

I’m not really sure when the birthday of the laser really is. Anybody know whether a single date is even relevant? Weren’t there classified projects that predated Maiman’s work? What about the MASER?

the edible laser

May 12, 2008 at 9:12 am | | history, nerd

The beginnings of the laser age must have been a fun time: crazy new experimental possibilities, beautiful optical demonstrations, dye lasers squirting carcinogens everywhere, and new lasing materials around every corner.

The “edible” laser is a great example:

High-gain directional stimulated emission has been observed for a number of dyes in gelatin with pumping by a nitrogen laser or a liquid dye laser. For some dyes the gel is made with water and gelatin; for others a detergent must be added or glycerin used instead of water. (Source: Hänsch, T.;  Pernier, M.;  Schawlow, A. IEEE Journal of Quantum Electronics 1971, 7, 45-46.)

I probably would not eat that for multiple reasons: I’m vegetarian, the detergents probably wouldn’t taste good, a nitrogen laser in the eye is unappetizing, and I doubt that fluorescein is food-grade. Theodore Hänsch describes some of these fun laser stories in Optics and Photonics News 2005, 16(2), 14-16 (or the PDF here).

It’s a fun read. Or just read the first page, then look at the pictures, like I did.

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