Category Archives: Media

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!

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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):

LUU Big Band Tour 2012

Some background info and assorted media (further down) from Tour 2012.

Band/Tour

Leeds University Union Big (formerly Dance) Band, which I play bass for and used to MD, just got back from the annual tour of France. This involves going to the same campsite near Bergerac every year, which is nice because it means the gigs we play around the area are always sold out.

Matt Yardley and George Millard are MD-ing from lead trumpet and lead alto respectively this year and have taken this year’s talented group of musicians further than I imagined the band would ever go musically, so well done them. Recordings featuring them are further down this post.

What has been most fortunate though is that this happened to coincide with the presidency of James Kelsall who has done more, and done it better, than any performance-group-leader I’ve ever met. At last year’s AGM, dressed up in period drama costumes on tour, he had two ambitious aims: record a studio album, go and play at the North Sea Jazz Festival. The CD, ‘Swingin[g] from the Treehouse’ is now becoming available, and in July we’re going to play at North Sea. Along the way we’ve also recorded music and video for ITV’s upcoming drama Mrs Biggs and on 12th May we’re bringing the very famous Liane Carroll to Leeds for a gig. It’s all pretty amazing and makes me very glad to have happened to be studying at Leeds this year. Well done JK!

Recordings

Here are some bootleg recordings from my phone and a few videos from tour.

Concerto for cootie — matt yardley, trumpet

Lovely Ellington chart, very very carefully arranged and excellently played. 2:39 onwards is pretty cry-y.

bei mir bist du schon — george millard, clarinet

Funny sort of dance hall style chart, the kind where on the video all the musicians’ bodies and smiling faces are perfectly stationary apart from e.g. drummer’s arm or conductor’s hands.

Samantha — George Millard, alto sax

(Featuring George on his main instrument.) Eyeshadow is even more fitting on this tune for some reason.

BBC Grandstand — arr. jj williamson

An arrangement I did a while ago to test out Sibelius 7 Sounds, finally finding use as a way to provide nostalgia for British ex-pats.

Under the sea — arr. jj williamson

I arranged this as a special request for a sea themed ball we did. Jamie Lambert’s vocals manage to be completely authentic without being racist at all.

Almost like being in love

Arrangement as done by Natalie Cole, and one of my favourite songs ever. Vocals from Loucin Moskofian.

At last

Power ballad time. Corine Sheratte singing, George Millard on sax again.

Cheese and carrots

Brilliant band chart. George Millard on alto again (my dad seems to prefer videoing tunes with him soloing), and Ciaran Diston on trumpet. Hugely appropriate tritone substitution at the end, well done me. Also featuring my dad and little sister arguing about who has the dubious privilege of holding the iPad.

Videos of my PhD, with OVITO

Philosophy…

Writing computer code for physics research is quite different to a lot of commercial software development (in a number of ways, which I might at some point write about in detail here).

For example, graphical output. In most consumer software, it’s usually pretty important to at least have a nice-looking graphical interface for the user. In special cases, e.g. games, the graphical (and aural) feedback is pretty much the whole point of the software, so it’s obviously important to get it right.

In scientific simulation, graphical feedback often doesn’t have quite the same status because it’s not normally the main output of the software. Instead, the main purpose of the code might be to produce huge data files which can then be analysed to measure various properties of the simulation’s ‘trajectory’, (e.g. temperature, pressure, structure) producing results broadly analogous to those taken in a real-life experiment. Whether or not the program looks good while it produces this trajectory is less important, and because speed and efficiency is usually such a key consideration in simulations, anything that might introduce an unnecessary overhead (e.g. graphics) is usually turned off.

However, in another way, graphics play an even more important role in scientific simulation — bug checking. In contrast to consumer software, where a bug might not matter as long as it has no observable effect or doesn’t crash the program, the value of scientific simulation code is completely tied up in knowing exactly what the code is doing. It’s no good thinking that a bug doesn’t matter as long as the results come out as expected, because the whole point is that you don’t know in advance what the results will be, and you’re interested in how they might differ from expectations. An interesting simulation result is no use at all if you’re not sure that the code, in microscopically fine detail, is doing what you say it is — the point of the simulation is to find out how large-scale effects emerge from known small-scale dynamics and if those small-scale dynamics are subject to errors and bugs, you probably won’t discover anything useful.

So, by visualising your simulation, you can check for bugs which might not be obvious during analysis. You can check that the individual particles or molecules or whatever are acting believably, as you programmed them to, and then be a lot more confident in any large-scale, emergent effects that you discover.

Also, more importantly, it looks cool.

OVITO

For a while I’ve been looking for an easy to use and powerful visualiser for atomistic simulations. I’ve used some not particularly fancy home-made code for this but wanted something more versatile that was still able to handle tens of thousands of particles.

So, OVITO which uses OpenGL rendering and is completely free and cross-platform, is perfect. I wrote some code that quickly converts my simulation’s data files (‘trajectories’) into a format readable by OVITO, loaded them in, and now I can spend all day making videos instead of doing real work. This program also easily allows special effects like color-coding particle properties, structure analysis, rotation/slicing of the simulation box etc., so it’ll be handy for preliminary analysis as well as making illustrative videos for seminars and so on.

An example

I recently posted about gas-liquid phase separation, specifically ‘spinodal decomposition’ in which the phase separation happens quickly throughout the whole system, rather than by nucleating at a specific site. A while ago I tried running something similar but in the presence of a template for crystal growth (i.e. a regular lattice at one end of the simulation box). This templated growth is another main focus of the project so we thought it might be interesting to combine the two ideas.

A video, produced with OVITO:

What seems to be happening for the parameters I’ve used is that the template causes a crystal to grow but, as was discussed in this paper, the crystal can’t locally coexist with the liquid, even though the liquid has a roughly similar density to the crystal. Instead, the crystal needs to coexist with the very-low-density gas phase, so it coats itself with a thick layer of gas which ‘shields’ the crystal from the liquid as it grows. It’s a ‘split interface’ (Crystal-Gas-Liquid) similar to those discussed here and may substantially slow down the growth of the crystal. Experimentally, this means that little crystallites form which effervesce, or bubble, as the gas bubble they keep trying to form around themselves floats away. It’s an inherently nonequilibrium effect because, at equilibrium, the gas-liquid separation disappears and you’re left with just two phases: a crystal and a very tenuous vapour. The effect of ‘metastable’ (nonequilibrium) phase transitions like the gas-liquid separation is a key focus of my work.

Research paper: Spinodal fractionation in a polydisperse square well fluid

EDITED: August 2012

The paper has been published in final form by Physical Review E — the final arXiv update is available here.

Here my first publication co-authored with Mike Evans. As well as being published in Physical Review E, it’s available on arXiv, which is freely accessible and contains copies of most of the papers published in recent years in a variety of physics and other fields. In fact, the conditions of my PhD funding explicitly require that my work has to be freely available — isn’t science good?

Most substances in soft matter (colloids, polymers, biological stuff and so on) are ‘polydisperse’ which, as explained here, means that all the constituent particles of a big container of the stuff are different in terms of e.g. their size or charge. This is in contrast to simple molecular fluids like water, in which every molecule of H2O is identical. Statistical mechanics and thermodynamics were originally designed for these simple fluids, so while they have been applied in soft matter with some success, traditional theories fail to capture some important and interesting phenomena in polydisperse materials.

For example, during phase separation, particles with different properties can end up being partitioned, or fractionated, into the different phases. In a simple example, a crystal growing from an initially disordered fluid of size-polydisperse particles might end up incorporating predominantly larger than average particles. This might not matter too much, but if you’re trying to create a precisely-characterised photonic crystal with a certain lattice parameter, it could matter quite a lot. Or, you might want the particles to fractionate between the phases, in order to then scoop out some of one phase and end up with a purer substance than you had before. In any case, it’s important to know how fractionation happens in polydisperse systems.

In the paper, we’ve simulated gas-liquid phase separation in a polydisperse fluid, and observed fractionation of particles between the two phases on a surprisingly short timescale. Even while the system is very quickly changing and coarsening its spinodal texture, particles of different sizes end up finding their way preferentially into one or the other phase. There’s also a striking dependence on a very trivial-seeming detail of the particle interaction, which ends up completely altering the observed ‘direction’ of the fractionation.

Fractionation has been measured in experiments, but the early stages of phase separation are very difficult to access because of how quickly the system is evolving. So, our simulations give a nice insight into how the final states observed in experiments are actually enacted through the course of the phase separation, and as far as we know constitute the first such measurements on a truly polydisperse model colloidal fluid. There are some nice pictures too.