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!
14 hours ago
Friday, June 21, 2013
Thursday, June 20, 2013
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!
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!
Wednesday, June 5, 2013
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......
Read more!
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......
Read more!
Friday, May 31, 2013
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.....
Read more!
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.....
Read more!
Sunday, May 5, 2013
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.
Read more!
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.
Read more!
Monday, January 7, 2013
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......
Read more!
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......
Read more!
Friday, December 21, 2012
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!
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!
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