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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