Sunday 25 August 2013

Calculating Carbyne

A group of researchers at Rice University have performed some nice calculations on carbyne, or linear acetylenic carbon, determining its mechanical properties and lots of other fun stuff. Carbyne is a carbon chain with alternating single and triple bonds, and therefore there's plenty of reason to expect that it'd have some interesting mechanical properties like being really strong. Of course, being basically a whole lot of acetylene molecules spaced apart by ethane, it's supposedly be really reactive, and it's strongly suspected that it'd cross-link to death if left to its own devices. (Alternatively, it could be double bonds all the way down; more on that later.)

The group did periodic DFT calculations in VASP to calculate the material's strength - when it breaks -  and Young's modulus, a measure of its resistance to stretching. If you're not familiar with periodic boundary conditions, imagine a Pac-Man or Asteroids game board. Everything that goes out one side wraps around to the other. So a snippet of the molecule sees an image of itself continuing at each of its own ends, and those ends in turn see their own duplicates, and so on. This is an excellent model of an infinitely long chain that doesn't change anywhere along its length. This model of an infinitely long chain is, itself, is a good approximation of a really long, but finite carbyne molecule - and by stretching that chain they could measure its Young's modulus.

They also did some molecular calculations on some rings of the material to estimate its resistance to bending, and on finite-length carbyne molecules (capped at the end with different functional groups) to measure its resistance to twisting. To finish it off they determined the energy barrier to cross-linking when two molecules come together, how well it conducts electricity, and whether the single-triple or double-double bond structures are preferred.

Thorough work!

It transpires that it's not only really rigid but spectacularly strong. Its Young's modulus is double that of the next stiffest material, graphene, and three times that of diamond. It's also comfortably stronger than either. That's right, if you're looking for something to build a space elevator cable out of, miles of nanotubes are no longer the cool hypothetical material to go for. Its resistance to bending and twisting are on a similar order of magnitude to double stranded DNA, a whopping great hydrogen- and covalent-bonded monster of a material. (Interestingly, carbyne's properties are strongly dependent upon what capping groups are used, which could make for some interesting fine-tuning.)

Fun stuff. The real question is, will it hang around when you make it?

Well by these calculations, when bringing two chains together there's an energy barrier of 0.6 eV to them cross-linking. That's pretty substantial. On the other hand, it's very unlikely that two carbyne molecules would just benignly wander up to each other like this. I suspect that when you put the molecule into a real-world soup of radicals and ions, it's not going to have a hard time finding a way around that wall. They also determined that two carbyne chains won't cross-link together down their whole length; the difficulty of pulling the two chains alongside means that there are alternating stretches of untouched and cross-linked carbyne. Again, I'm not sure that carbyne would behave itself quite so well in the messy real world, but it's promising.

You can read the paper at Arxiv, "Carbyne from first principles: Chain of C atoms, a nanorod or a nanorope?" by Mingjie Liu, Vasilii I. Artyukhov, Hoonkyung Lee, Fangbo Xu, and Boris I. Yakobson; a quick Google News search for Carbyne should give you plenty of news coverage.

As always, all errors here are my own, and I would be really grateful for any corrections you might want to send my way.

Tuesday 20 August 2013

When someone says "formula for the perfect", I reach for my red pen

Since this morning, I've upgraded my reaction to the RSC's formula for the perfect cheese on toast from "not impressed" to "deeply not impressed".

It starts off pretty well. They actually did some experimentation, which is a far cry from most "formula stories" cut from whole cloth at a PR firm's behest, many of them from the same few chronically underworked researchers. By carefully varying the amount and type of cheese, the thickness and type of bread, and the distance from the heat source, they determined the combination most appealing to a panel of experts. That's how science is done! Science is about thinking and experimentation, which are really, really accessible, so a cheese on toast experiment was a great idea. People could recreate this test at home. (And I encourage you to!) Great job RSC.

Then they present the results like this:

That's not okay!

By cloaking their results it in a mish-mash of confusing abbreviations, the formula just continues the message that science is an opaque and needlessly complicated field, making grand prognostications about topics in which it is hardly the be-all and end-all of judgement. You wouldn't actually write a reaction like that in a report, anyway - it would defeat the purpose. They take less space to simply tell us how to make the cheese on toast, and with more clarity, than the diagram occupies. So it's not just complicated, it's inauthentically complicated!

Outreach efforts like these should show that science is an activity for everyone, and do their best to explain that when scientists use jargon, it's only when needed for clarity or precision. Science can be, and should be, universal. Science is about trying things out, testing and iterating. We can all do that, even if we're just trying to figure out the best way to make our favourite snack.

Here's an equation I think we can all get behind:

Cheese + bread ---SCIENCE---> Deliciousness

For good articles on bad formulas, you could do worse than start with these:

"Transparent excuse for printing a nice pair of hooters" by Ben Goldacre
"X+Y/Z=BS" by Dan Rutter
"Formulaic fashioning of fun formulas" by Marc Abrahams
"Stupid formulae" by Andrew Taylor.

Monday 5 August 2013

A Chemical Imbalance

Professor Polly Arnold of the University of Edinburgh department of chemistry is launching a campaign to understand and improve gender equality in science titled "A Chemical Imbalance" which the BBC have written a story about. She's taken Rosalind Franklin award funding and used it to produce a free movie and eBook, hosted on the Chemical Imbalance web site. Full disclosure, I'm knackered and preoccupied with work right now so I've not had a chance to check out either in any depth. However the campaign clued me in on an Edinburgh science story that feels familiar (perhaps via the Surgeon's Hall museum) but I never learned about in any depth: the Edinburgh Seven.

The Seven were a group of women, led by Sophia Jex-Blake, who banded together so that they could be allowed to study for degrees at the venerable old University of Edinburgh medical school in the late 1800s. Despite their successful studies, performed in the face of opposition from science notables like Alexander Crum Brown - later president of the RSC - and an actual riot about their anatomy exams, the university refused to allow them to graduate. Most of them ultimately went on to be granted medical degrees by more progressive institutions, and blazed a trail for future equality in education and medicine. You can read more about them in the eBook on the site, or if that's too long, Wikipedia and this blog.

With a wonderful sense of cosmic justice, Professor Arnold is now the Crum Brown Chair of Chemistry, while Professor Lesley Yellowlees was not only the first female head of chemistry at Edinburgh, but is now the first female president of the Royal Society of Chemistry, a position once held by Crum Brown himself.

Such overt discrimination has waned in much of the world, but the gender balance in the sciences is still ridiculous. The chart on the site shows the ridiculous drop-off rate between undergraduate, where it's nearly equal, and professor, where it's ten to one. Worse, as Prof. Yellowlees relates in the BBC article, outward contempt for female scientists is still depressingly extant. I'm not sure what I can do to help, but passing it along, reading the book and watching the documentary seem like a good start.