Ahh, this old thing.

dusts off the blog  Ahh, there we go.

Still at the same job I started last year, and managed to avoid getting 'rightsized' this time around.  I suppose since my job involves doing the work that is required for the final payments by the customer, I'm safe for a short while.  Of course, due to 'rightsizing', I've got additional work to do to help make up for the absence of those who did get 'rightsized.'

Sadly, I've realized I can't say much more about what I'm doing, as I'm fairly sure it will out my identity.  Alas.

P.S. - I have figured out that I dislike driving in the Boston/Cambridge area a great deal, though. Read more!

2014 Nobel Prize in Chemistry Hijacked by Physicists

This year, all three laureates are physicists!  All three earned their doctoral degrees in physics, after all.   And 'super-resolved fluorescence microscopy' - come on, that doesn't sound chemical at all! 

Where is the outrage? 

:) Read more!

Oddly inspired.

I'm...it's really bad timing, but a recent article I found on a blog has inspired me to write about actual science.  Sadly, due to the combined effect of my ongoing relocation and next week's planned schedule, you will have to wait until September to read about it. 

Which, you know, given that it looks like yet another project I've worked on has hit the "this isn't getting published" zone from my past postdoctoral position (I had one in grad school, despite yearly attempts for about four years after graduating to get my advisor to act in some positive manner towards it), is saying something.

In short, I think the trick is to select research projects that require effort to progress - not effort to keep them from collapsing into a singularity from which nothing can escape. 



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Capitalism.

My non-research career seems to be going well, at least insofar as I can manage to say 2.5 months into it.  Relocation will occur in August, and I will be able to reduce the amount of time I spend on the current commute.  It's been quite an experience, and to be honest, I think it will keep me from being bored for a couple of years at the very least.  

Talk to me in a year, though. Read more!

A quick note.

I have escaped the chains of academia and will be gainfully employed in the private sector starting later this month. 

Still on the East Coast, though.  Can't win them all.

I may get around to more regular posting in the future, although that will depend on timing and cognitive momentum.  Read more!

Nobel Week

It's been an interesting week so far, with the vesicle transport, Higgs boson, and now multiscale modeling being recognized.   While I clearly missed the ball this year in contrast to last year, I suppose it still leaves a potential Prize for molecular dynamics to be awarded in Chemistry, or perhaps Physics without the Higgs juggernaut lying in wait.

Of course, I am tremendously entertained to see the "those three do a lot of biological applications" comments already cropping up elsewhere.  Heh.   Read more!

Another really short lit link post.

A cavity QED approach to magnetic resonance that was just published - figured a few of you might be interested in this sort of thing. 

In other news, have a fair amount of NMR data myself to work through and understand.  Speaking of which, back to it. Read more!

Still alive....

You can cue the "Portal" song here - trying to not fall entirely away from this blog, especially as the most entertaining time of the year approaches for the chemical blogosphere.

Here's something for the quantum mechanics & photosynthesis fans - Excitation Energy Transfer in a Classical Analogue of Photosynthetic Antennae from J. Phys. Chem. B.  

I may have more to say about this and other things in the future.  In other news, I suppose we'll all be really careful with our supplemental information sections in the future........ Read more!

Back again....

Yet another "quantum effects in photosynthesis" paper.

Waiting for the rampant speculation that can arise from this paper, as well.

Off to troubleshooting the remainder of my afternoon! Read more!

A neat bit of work.

From the people who brought you a structure of an unengineered full-length GPCR in phospholipid bilayers comes a structure of an unengineered full-length mercury transporter in phospholipid bilayers.  Gotta say that this is pretty neat.....

While new technical difficulties are otherwise occupying my efforts, I have enough things in the air to keep me busy.  Speaking of which, back to it! Read more!

Trifling Thoughts.

1.) I really was hoping to go for a couple of more years before having to deal with a poorly behaving high-power RF amplifier.

2.) Whenever someone says that quantum mechanics should be understood at an intuitive level, I wonder if they never had to occasionally take solace in the mathematics earlier on in their education.  While it was fleeting during intro E&M at university, the intermediate E&M class did have me routinely finding some sanity in mathematics.  Perhaps my intuition is just exceptionally poor, of course. 

3.)  Given all the hoo-ha about AFM recently, I thought this was interesting and timely.

And there's a good ending point for today......


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Angry Birds: Academia

The title is just what I think would be a thoroughly hilarious game for one's smartphone.  However, as I am a cranky postdoc (at least until early next year), I have found the franchise thoroughly helpful for those moments where I need to kill a minute or four in lab waiting for something to incubate/boil/equilibrate.

While I am tremendously interested in chemical microscopy of all sorts, various online discussions of a recent Science paper regarding AFM studies of single molecules of reactant and products reminded me of the somewhat odd excitement over "seeing" something.  Your eyes are limited spectrometers that can only deal with photons, and many don't appreciate the signal processing involved between your eye and your brain.  Now, if we could do electrons and neutrons as well, I'd be less worried about our restricted optical window.  Heh.

I keep meaning to post long overwrought thoughts about NMR, lipid bilayers, and the scurrilous treatment of valence bond theory by some people, but don't hold your breath.  Maybe once I clear my to-do list further, I'll have the cognitive energy to do so.

Question for any who might be reading - is there an opposite of "minimal publishable unit"?  When you have a ~ 15 page article in a solid journal along with another ~ 15 pages of supplementary information, maybe you want to see about splitting that work up.  Especially if you're citing the SI in the main article. 

I'll go topple over some structures now.....






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A bit overdue, I suppose.

It seems that I have neglected you, dear blog.  I would express my regret, but, well, I've been busy.  I do hope that any occasional visitors have been having themselves a healthy, enjoyable, and productive 2013.

In any case, research is progressing to the point to where critical experiments will be run within the next few months, and presuming that my calculations are not too far off, we should obtain a reasonable amount of interesting data that will be published not long thereafter.   Which should help with the entire "what to do next?" conundrum.

However, before I meander to other topics, an observation - the one thing that keeps biochemistry challenging is that your samples are never entirely happy.  You can purify it to some vague approximation of homogenity, put it in a buffer it likes, add cryoprotectant, and flash freeze in countless little aliquots for storage at -80 degrees Celsius.  And when someone takes out an untouched aliquot 3 years later to check its viabiity, they find it's.....reluctantly alive.  You compare it to a sample made of protein you prepared a week ago, it's clearly working nowhere near its potential.  Now, I had the occasion to stop by my old grad school lab the other year, and the one student working on my old project is still using the small molecule ligands that was synthesized by myself and another student ~ 10 years ago. And that sample was not aliquoted out in tiny volumes, each one to only be used once, rest assured. 

Onto said other topics......

- I have to say I am extremely tickled and intrigued by the idea of approaching quantum mechanics as a certain generalization of probability theory.  It's probably a good thing I have no intentions of being a faculty member anywhere, as I'd probably try to pull off a presentation like this to students. 

- I sort of postponed my entire relativistic quantum chemistry self-study program.  I will get back to it.  One of these days.

- I am finding myself in the position where I need to start doing some serious practical and theoretical NMR teaching to a very small audience, though.   The whiteboards in lab are going to get messy, I suspect.

- Should probably start microblogging more often, to boot. 

Anyway, going to try and chime in more regularly here over the upcoming weeks and months. 




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Starting off 2013.....

I hope that everyone's 2013 looks to be promising and full of potential in all possible areas.

While I did manage to post more in 2012, I think more substantive/research literature-oriented posts are called for here.  I suppose I should look into figuring out how to insert well-formatted equations to help with this goal, although I suspect I will find it easier to just generate the equations elsewhere and then insert them as images.  I do not expect to accurately predict one of the Nobel Prizes again, though. 

I contemplating bringing up the ACS panel suggestion to have people complete a doctoral degree in 4 (no more than 5) years to a couple of biological chemistry faculty I know, but I realized that this would cause such severe trauma they'd never recover.  Because - thankfully, this wasn't me - I know people who did a Ph.D. in chemistry (bio focus) who did take 8 or 9 years to finish the degree, and they were uniformly in certain labs whose aspirations were borderline insane.  If it takes your students that long to finish a Ph.D., you are doing something wrong.

We will see how far I get with my various scientific self-improvement goals this year (read up on relativistic QM/QC - I have a borrowed copy of Dyall & Faegri's text, kind of poking through it slowly; my going-on-a-couple-years goal of getting Shaik & Hiberty's text on VB theory under my belt; and more on my various programming self-study projects).

And now back to pushing the limits of knowledge further......

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Off the back burner.....

Meant to post about this a while back, but never quite got around to mentioning it.

Lipid Bilayers and Membrane Dynamics: Insight into Thickness Fluctuations.

I suspect anyone reading this post knows that membranes are far from static entities, ranging from lateral diffusion of individual lipids within the bilayer to collective motions of the membrane. Here, the authors report of a thickness fluctuation, which is exactly what it sounds like -

From here.

The authors utilized both small-angle neutron scattering and neutron spin echo spectroscopy on these samples, as neutrons offer remarkable versatility in terms of probing various length and energy scales, as is presented here -

In any case, I thought it was interesting.  They are - based on what I've heard - looking at lipid bilayers with proteins, but I haven't seen it come out yet in the literature.  I think as people become more interested in what is really going on in complex biological systems, we're going to need to look beyond the purely molecular length and energy scales to the mesoscopic regime (however one defines it).

Happy holidays and New Year to all! Read more!

Speak of the devil....

...and the devil, he shall appear.

A recent discussion at the Curious Wavefunction briefly touched upon the role of (macro)molecular crowding in biochemical studies.  I am presently preparing to see whether a certain set of experiments are feasible, and in some of the potential tests, I am adding a fair amount of crowding agents to my samples. 

The samples that have those crowding agents are presently the only ones that exhibit any enzymatic activity.  The other samples are dead, biochemically speaking.  One of the "dead" samples does exhibit complex formation in one of my alternate tests, but that's it.  Further tests are needed, of course, and it's certainly possible that I can retain enzymatic activity in the other samples upon logically adjusting my current protocols.  But perhaps there's a lesson here to be learned.




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Lit Links

So, in case any were wondering, my area on the East Coast was mostly spared the wrath of Hurricane to Post-Tropical Cyclone Sandy.  Some rain, a bit more wind, but not many power outages in the immediate area.  I am however fairly well prepared for any mystery zombie apocalypses that might arise (from the dead).  I hope that all of you reading who were subject to its furor endured the storm as well as possible.

In any case, some bits of possible interest -

1.) PNAS has a special feature this week on "the Chemical Physics of Protein Folding."  Sadly, it's behind a paywall for the time being.

1.5.) Related to this, I once mentioned a while back in a comment (I believe over at the Inquisitive Ket) about one of the less-important reasons Levinthal's paradox never really bothered me, namely, that proteins aren't really free to sample all possible conformations due to their interactions with other proteins (even indirectly due to crowding), the solvent, and with itself.  In any case, it's always interesting to see people carefully examine these sorts of questions in the recent literature.  

2.) Gaining structural insight occasionally takes a while.  It also reminds me of the utility of neutron science for biochemistry - the ability to use contrast variation using selective deuteration make it possible to probe multicomponent systems.  And let's not forget that one can also use neutrons for spectroscopic measurements. 

Anyway, back to the actual science…..  Read more!

Chiming in with a #ChemCoach entry

Here's my contribution to the ChemCoach Carnival, for what it's worth.


Your current job.

I am a postdoc in an actual chemistry department on the East Coast (USA) doing a mix of physical chemistry, biochemistry, and spectroscopy, along with dashes of molecular biology, computation, and misery. 

What you do in a standard "work day."

No such thing as a standard work day for me -  I'm presently slogging through heaps of molecular biology in order to validate a protocol for producing uniformly 13C/15N labeled protein (mostly since my PI isn't yet comfortable with how we do things in the 21st century).  Earlier this year, for example, I was doing everything from NMR on inorganic solids (after effecting some probe repairs on my own) as well as some p. chem. of lipid mixtures, in addition to protein NMR (solution and solid state). 

What kind of schooling / training / experience helped you get there?

 I was a biochem/chem undergrad (did my undergrad research in a biophysics lab - lasers and magnets, what more could one wish for?) and did my Ph.D. in an honest-to-Buddha chemistry department, doing biophysical chemistry.  I was briefly diverted into a year at a cancer research institute doing biophysics/soft matter-oriented work (that was a trip, let me tell you), but returned to my chemical roots. 

How does chemistry inform your work?

Just the other day I was trying to get this horrendous mix of inorganic chemicals to go into and stay in solution, actually - and people say there is no chemistry in biochemistry!  Heh.   My perspective on many of my scientific interests is rooted in my chemical background - for example, signal transduction could be translated as essentially controlling the rates of chemical reactions across interfaces, after all.  It's a rather essential component of what I do on a daily basis.

Finally, a unique, interesting, or funny anecdote about your career

I was at a conference where I spoke to the colleague of this scientist who had written a paper I had read and digested multiple times, as it was extremely germane to my interests.  He noted that said scientist had never followed up on this particular aspect since they found that obtaining reproducible data was far too tricky.  I should have realized then that my project might have been a bit ambitious, but I persevered and did manage to get reproducible data.  It just took another 2.5 years on top of the 2 years I had spent working on said project.....  Read more!

Some minor notes.

The reason they're making your son take chemistry?  Because they're mean.  Or perhaps because they hold to some archaic notion that education is about broadening one's horizons and tempering the intellect, not just about preparing one for any particular career path.  I haven't decided. 

Small-molecule synthetic chemistry in the NY Times?   A pleasant surprise to see in the national newspaper of record, at least last I checked. 

Microbial physiology via NMR.  So cool.   Also, kind of jealous.  I really need to get some awesome stuff done sooner rather than later.

I think that will be all for the evening.


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Prize ponderings

There have been some particularly interesting and worthwhile points made on the blogosphere over the last two days in the wake of the Nobel announcements.

1.) The success of small/investigator-driven/table-top science.  Actually, this applies to more than just the Chemistry Prize - see here for some comments regarding this year's Physics Prize. 

2.) Are we doing ourselves a disservice by discussing and debating the Nobel ad infinitum?  Is trying to find one to three people to recognize for a certain (set of) accomplishments really the best option?  How much of this is a holdover from how science used to be conducted pre-1900?  I happen to especially like Paul's Chemical Hall of Fame idea, and am willing to participate.  (I may want to nominate a physicist or two, though.*)

3.) Chemjobber brings up the interesting point as to whether the "mix" of chemistry that gets highlighted due to the Prize announcements is the one the community wants to present to the public. 

4.) There seems to be a sense that we need to circle the wagons a bit before the central science withers away.  I can't entirely disagree with this one.  I've been told multiple times that some of the questions I've stumbled over while doing biological chemistry regarding underlying questions of (mostly) physical and inorganic chemistry aren't really fundable, at least relative to the biological question with which I'm engaged.  You can only try and spin questions into applications for so long and so far before it gets tedious.


5.) I would read this post over at Everyday Scientist if you haven't already.  I'm in the same sort of boat as a bio/physical chemist.  I look at the Physiology/Medicine Prize and see work like in vitro fertilization and the H. pylori work recognized, and vast amounts of cell biology and systems physiology in their ranks (immunology, olfaction, neurobiology, and so on).  I view biochemistry as something which is securely rooted within the realm of chemistry.  Of course, this makes me wonder - while the issue of communicating chemistry to the public has been a discussion topic in various contexts over the years, maybe we also need to open up the lines of communications between chemists.  I'm not entirely sure how to go about doing this right at the moment, but I am definitely open to ideas.  

Of course, perhaps this is all just colored by my spectroscopic tendencies - if I can fit it into a coil,  cuvette, or beamline, consider my interest piqued.  Biological, chemical, geological, material, or physical. 

As always, the comment section is open. 

*: Erwin Hahn and Albert Overhauser.  Spin echoes and the Overhauser effect.  You know you want to agree with me! Read more!