Category Archives: Media

Research publication: Registered/Antiregistered phase separation in bilayers

A couple of days ago, the April 21st 2015 issue of Biophysical Journal came out. My first paper with Peter Olmsted appears within and is featured on the cover! We studied the effects of inter-leaflet coupling in bilayers, and found fascinating kinetics driven by competing stable and metastable phase coexistences, involving registered (symmetric) and antiregistered lipid domains. I won’t go into more detail here, there is a blog post on the Biophysical Society Blog that tells you more.

Cover Image

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Gone imagin’

I’ve recently been feeling more like an intern at Pixar than a scientist — yes, it’s time for some scientific imaging. In my field of simulation and theory, some form of imaging is important in a prosaic kind of way just to get a feel for what’s going on, and check for any disastrous bugs. But, more and more, it’s becoming a real mode of scientific communication. Journal covers commonly feature simulation renderings or even schematic artists’ impressions, as well as more traditional fare such as beautiful microscopy images. With the move towards online journal viewing (and sometimes, free colour printing), authors have more and more freedom to include beautiful renderings as a key, functional part of their scientific story.

I mostly use the incredibly versatile and intuitive OVITO package for the purpose. Recently I spent a while learning its intricacies (for example, the software Tachyon renderer for nice directional lighting). Here are a couple of images from the two main strands of my work. OVITO does a great job with both a typical 3D particle based simulation, and a quasi-3D rendering of a 2D lattice model with highly stylised cubic particles.

Colloids 

First up, phase separation in polydisperse colloids. My latest paper in this area focused on methods of characterising the highly complex phase compositions and kinetics involved. The colours are computed from our new approach to measuring local concentration when a large spread of particle sizes exist, which turns out to be quite a subtle problem. The picture really helps get across just how highly polydisperse the fluid is, and we can even see by eye the way that larger particles, in this case, end up in the denser (liquid, hot colours) regions. Of course, all of this is supplemented with quantitative measurement and graphs, and the message could be got across without this picture. But: it’s beautiful; and it gives the reader an instinctive feel for both the setting of the work, and one of its key findings. The image was shortlisted as a J. Chem. Phys. cover image.

Gas-liquid phase separation in a highly polydisperse simulated fluid. Novel characterisation methods are used to study which particles end up where.
Gas-liquid phase separation in a highly polydisperse simulated fluid. Novel characterisation methods are used to study which particles end up where.

Membranes

Our manuscript in review [now accepted in Biophys. J.] provides a theory for how lipid bilayer domains do or don’t align between the leaflets. In fact, the theory began as a simulation — an idealised lattice model capturing a key physical feature, the thickness of the bilayer leaflets. It turned out to be idealised enough for pen-and-paper treatment, hence the resulting theory. But, directly simulating the model helps to corroborate the results and figure out what goes on over longer timescales that aren’t treated in the theory. Mapping membrane thickness as the z-coordinate allows the 2D simulation to be rendered in a quasi-3D manner, and the competing thicker and thinner phases can be seen nicely. OVITO allows cubic particles to be plotted. I used this to emphasise the underlying lattice nature of the model, but had the particles overlap in a ‘random-looking’ way partly for artistry, and partly to get across the fluctuating, messy nature of liquid phases in the bilayer at the molecular scale. The image was a finalist at the image contest of Biophysical Society’s annual meeting, and I came away with a nice big hard-back printed version to mount on the wall.

Rendering of an idealised lattice model for a lipid bilayer membrane. Separation into multiple metastable and equilibrium phases is possible due to the interaction between the bilayer's two leaflets. https://scholar.google.com/citations?view_op=view_citation&hl=en&user=6M4KATQAAAAJ&citation_for_view=6M4KATQAAAAJ:UeHWp8X0CEIC
Rendering of an idealised lattice model for a lipid bilayer membrane. Separation into multiple metastable and equilibrium phases is possible due to the interaction between the bilayer’s two leaflets.

Recordings + Charts from Ben/George/Martin/John/Chief

Yo.

A few weeks ago I did my second-to-last gig in the UK, for a change leading a project and so being able to choose some tunes I’d always wanted to play but hadn’t. It was lovely to have some great friends in the audience, and in the band. George Millard kindly came up from London, and he and Ben brought some nice songs along too. There were lots of contrafacts, lots of bop and a few lovely ballads. I’ve uploaded a selection to a Soundcloud set and am making the PDFs available too. I just zipped up the folder containing the charts but it’s pretty easy to see how they fit together. Hopefully they’ll save people having to transcribe some of the less well-known ones themselves. Do tell me if you end up using them, it’d be nice to know.

Charts

Statistical physics: Mike Evans’ physicsfocus blog

My old PhD supervisor, Mike Evans, is an occasional writer for the Sky At Night magazine and also blogs for physicsfocus. A quick look at his writing in either of these settings demonstrates that as well as being an expert in his field (which, broadly, is mine), he’s something of a philosopher with a very wide range of scientific interests.

However, this post finds Mike writing on the subject closest to his professional heart: statistical physics. This branch of physics is fundamental to our understanding of the world because it deals with situations where we have more than “just a few” of a particular entity. Considering that something as simple as a glass of water comprises billions and billions of mutually interacting and constantly moving water molecules, its clearly important to have an approach that is practical in these cases.

Further, statistical physics unifies things: a vast cloud of cosmic dust is quite different to a small tube of a colloidal suspension. But they’re similar in some ways. One of these ways is that on the tiniest length scales, they’re both made of protons, neutrons, and electrons. But, as Mike nicely points out, this misses the (thermodynamically) large picture: the two systems are also similar in that they both contain a very large number of their constituent particles, so that statistics governs their large-scale behaviour. In fact, this is arguably their most important similarity. Read the post to learn more about universality in statistical physics.

 

For anyone who wants some exceedingly clear and enjoyable insights into the life of a professional scientist, I can’t recommend Mike’s writing enough. Check out his personal blog too!

Lee Konitz transcription — “Two not one”

Here’s an amazing Lennie Tristano contrafact from the album “Lee Konitz with Warne Marsh”, based roughly on “Almost like being in love”. It’s one of those lovely tunes that starts on the subdominant — always good in my book — and is one of the nicest collections of mezzo forte quavers ever put together. Enjoy!

Lee Konitz – Two Not One

twonotone_concert

twonotone_alto

Research publication — The effects of polydispersity and metastability on crystal growth kinetics

Mike Evans and I have just published our second article together, in the Royal Society of Chemistry’s interdisciplinary journal Soft Matter. It concerns a simulation study of crystal growth in the presence of two common complicating factors: i) Polydispersity (particles are non-identical) and ii) Metastability (in addition to the crystal growth, non-equilibrium gas-liquid separation is taking place). The result is the “boiled-egg” growth mechanism, which we model with theory and simulation, and whose effects on growth depend on a subtle interplay between the two factors I just mentioned, which remains to be further explored. The work is of generic relevance to many situations, but particular examples include e.g. protein crystallisation, photonic crystal growth, colloid-polymer mixtures. There are looooooads of nice pictures in this one.

  • The advance online article is here.
  • A pre-print which I will shortly update with the final small changes we made before publication (freely accessible to everyone but with less pretty formatting and editing etc.) is here.

Enjoy!

 

Laurence Cottle transcription — ‘Quite Firm’

The stats on my site tell me a few things. One is that, particularly on Fridays, my visitors are predominantly Gardener’s World fans who have arrived here through the TV show’s ‘Community’ page on the BBC website, thanks to a pretty nothingy post I wrote about it one time. It has 33 comments.

Another thing is that quite a few people get here by searching for ‘Laurence Cottle transcription’ (brave souls), which is the kind of visit I’d prefer to encourage. So…

Here’s a transcription — the hideously fiddly yet actually quite listenable bass part from Laurence Cottle’s ‘Quite Firm’. There’s a few versions of the track on his website, a couple on the big band album and a small band one from ‘Live!’. I’ve used the Live! version as a template and transcribed the head. It’s really good writing, fits in brilliantly with the horn lines and in a perverse sort of way falls quite nicely under the fingers — definitely a bass player’s line. Here’s the PDF:

Quite Firm – Bass Guitar

And here’s a clip of me just about getting through the A and B sections (playing along to the ‘Bonus’ version from big band album, because the Live! one is out of tune with A=440Hz):