Journal Club: A New Blog

I've just started a new blog www.scmjournalclub.org. It's definitely in what you'd call the beta phase right now. I will certainly be changing the layout and gradually adding more permanent content over the next few weeks.

Contributions welcome to submissions@scmjournalclub.org.

While I do sometimes get a bit technical, Kinetically Constrained is hopefully of interest to people inside and outside of the field. The idea for the journal club is that it is aimed at people working in the area of soft matter and statistical mechanics. In particular I want it to be useful for postgraduate students who would find it helpful understanding papers they may have found a bit impenetrable otherwise.

How it will all work will hopefully evolve. I hope one day enough people check it out that the following scenario happens. A PG student presents a paper as best they can that they might be having trouble understanding. A comment thread follows and the problems get sorted out. Everyone wins.

I also suspect that hundreds of journal clubs happen each week in different universities. While I understand people might not want this to be public, for those that don't mind they could put their presentation on SCM journal club where it can benefit even more people.

To kick things off I've started with a recent paper on the arXiv by Andrés Santos on one of my favourite topics – hard spheres.

Brief Summary
In liquid-state theory the hard sphere equation of state is of particular importance because it is a fantastic reference system for a whole host of molecular and in particular colloidal liquids. The hard sphere equation of state (EoS) tells you what pressure you need to compress a your spheres to get a given density. With an analytical form for the EoS one can calculate any thermodynamic property one desires.

Percus-Yevick (PY) is a way to close to the Ornstein-Zernicke (OZ) equation – an exact relation between correlation functions – and is usually solved by either the compressibility route or the virial route. You’re basically choosing how your approximation enters. Here Santos has taken a different route, following the chemical potential, and it gives a slightly different closure to OZ.

Carnahan-Starling is an incredibly simple EoS for hard spheres which is in common use (fluid phase). It can be written as a 1/3-2/3 mix of the compressibility and virial PY routes. In a similar way Santos writes a 2/5-3/5 mix of compressibility and chemical potential routes and gets a similarly simple expression – which is ever-so-slightly better than Carnahan-Starling.

I'm more than happy to take contributions. I think it's nicer if people say who they are but I'll hold back the name if that's the barrier to submitting (provided it's not an anonymous destruction of a rival's paper). You can submit via submissions@scmjournalclub.org. For interested regulars I can look into direct posting via blogger.

Just hurry up and sit down!

As a semi frequent flyer, and incredibly impatient stand-behinderer I couldn't resist linking to this - Time needed to board an airplane: A power law and the structure behind it from a Norwegian group, Vidar Frette and Per Hemmer.

Boarding strategy is of great importance to airlines, where the turn around time of planes – especially short haul – can make a real dent in profits. For the authors of this paper, however, it seems they just think it's a neat model to test out 1D problems where the particles are distinguishable, rather than the more common indistinguishable particles. In a traffic model the cars are usually identical, whereas here the passengers have a specific seat booking. Statistically this makes a difference.

Of course many people do look at specific strategies. For example here, it seems that it's difficult to think up a strategy that beats random loading. One would think that loading back-to-front would be better but this is not the case. A quick google search finds this nice page from Menkes van den Briel. There you can see videos of all the different strategies.

Unfortunately the best strategy seems to involve seating people in order of window/middle/aisle. Not great if you're sitting next to your kids.

All of which did remind me that it is much quicker boarding when you don't have seat bookings. When I fly to England using a certain orange-themed airline, that doesn't book seats, there's an initial mêlée followed by reasonably rapid sitting down. On a certain royal blue-themed airline it takes forever for a plane half the size to get sat down.

My suggestion is that I should be allowed to starting poking, with increasing frequency and verbal abuse, anyone that I deem to be taking too long to put their bag away.

Clustering in sea-ice floes

I started writing this post as a long winded account of the difference between equilibrium and non-equilibrium statistical mechanics. It turns out that that is hard to discuss without waffling on, so instead I will just talk about an interesting paper from the world out of equilibrium - which is most of the real world.

I've been walking around with this interesting paper, "Molecular-dynamics simulation of clustering processes in sea-ice floes" by Agnieszka Herman, in my bag since November. It was picked up in the spotlight section, in Phys. Rev. E (loosely the stat-mech/complexity section). My attention was grabbed by the idea that simple ideas in granular gases could hold sway in the icy seas of the Arctic.

Marginal ice zone

Roughly speaking, it's always icy at the top of the earth and then as you go south it turns into ocean. Around the transition between icy and not icy (only the best technical explanations for my readers) is the so called marginal ice zone (MIZ). This is where bits of ice break away from the main ice pack and float around in the sea. Understanding how this ice moves around, and the effect of external forcing, is important if we're to best understand the impact of global climate change.

The ice-floes studied in this paper are in an intermediate region between densely packed and very low density. The sizes of the ice fragments are roughly distributed with a power-law tail and they float about and hit each other inelastically. It is here that one can make the link to something closer to my own field, it is a 2D granular gas.

Granular gases

In the world of the small everything is constantly being battered by random thermal noise. It's so random that it, in fact, becomes rather predictable and Boltzmann distributed. In the world of a bit bigger, this thermal noise doesn't really affect the individual particles any more and we're now dealing with grains. I've talked about this before in the context of colloids – the last bastion of thermodynamics before everything goes granular.

In a granular context the ice fragments are particles that move ballistically in between collisions, and when they collide energy is lost. This system, of dissipative colliding grains is known to have interesting dynamics including the clustering of particles and other complicated correlations.

The really nice thing about this paper is that what Agnieszka Herman has done is to simulate such a granular gas, but adding in realistic numbers for all sorts of effects such as friction, wind, currents, restitution coefficient (how inelastic it is) and to see if it can reproduce what is observed in the oceans. This can not have been easy to set up!

Comparing to real life

The image below is the sort of sea ice clustering that is seen in the MIZ. One sees that the smaller floes tend to accumulate on one side of the larger floes.

This is also seen in the simulations results. This is because, as well as losing energy in collisions, the floes are being driven by wind and currents. The larger floes catch up with the smaller ones pushing them along for a while until they fall off. The colour bar shows the velocities of the different floes.

At higher densities – more collisions – you can still see the gaps behind the large floes, although the distribution of velocities is now narrower.

I don't know how rigid this system is, it'd be interesting to know if there's a breakout point where the ice floes can suddenly escape. It's really neat to think that you can connect such different systems, not to mention such different scales, and still be able to say something sensible.

Big thanks to Agnieszka for providing the colour images. Images, copyright APS, are reproduced with permission from the paper Phys. Rev. E 84, 056104 (2011).

Networks in Nature Physics

For those with access, looks like Nature Physics has a complexity issue. With articles by Barabási and Newman and the likes, it looks like it has a solid networks bent.

There's a paper on community structure by my favourite physicist, Mark Newman, that I'm looking forward to reading.

Enjoy!

Lipid membranes on the arXiv

A while ago I discussed lipid membranes and how they could exhibit critical behaviour. There were some lovely pictures on criticality on giant unilamellar vesicles (GUVs) which are sort of model cell walls. That work was done by Sarah Keller and friends in Seattle.

This morning on the arXiv I saw this new paper, also by Sarah:

Dynamic critical exponent in a 2D lipid membrane with conserved order parameter

They look at the critical dynamics of the GUV's surface. Being embedded in a 3D fluid does have its consequences so they've attempted to account for the effect of hydrodynamic interactions. I haven't poured over their model but the paper looks really nice.

Paper review: Hexatic phases in 2D

I'm doing my journal club on this paper by Etienne Bernard and Werner Krauth at ENS in Paris:

First-order liquid-hexatic phase transition in hard disks

So I thought that instead of making pen-and-paper notes I'd make them here so that you, my huge following, can join in. If you want we can do it proper journal club style in the comments. For now, here's my piece.

Phase transitions in 2D

Dimension two is the lowest dimension we see phase transitions. In one dimension there just aren't enough connections between the different particles – or spins, or whatever we have – to build up the necessary correlations to beat temperature. In three dimensions there are loads of paths between A and B and the correlations really get going. We get crisp phase transitions and materials will readily gain long range order. Interestingly, while it should be easier and easier to form crystals in higher dimensions there do exist pesky glass transitions that get worse with increasing dimension. But I digress.

In two dimensions slightly strange things can happen. For one thing, while we can build nice crystals they are never quite as good as the ones you can get in 3D. What do I mean by this? Well in 3D I can give you the position of one particle and then the direction of the lattice vectors and you can predict exactly where every particle in the box will sit (save a bit of thermal wiggling). In 2D we get close, if I give you the position and lattice vectors then that defines the relative position and orientation for a long way – but not everywhere.

By "a long way" I mean correlations decay algebraically (distance to the power something) rather than exponentially (something to the power distance), which would be short ranged. We can call it quasi-long ranged.

Never-the-less, this defines a solid phase and this solid can melt into a liquid (no long range order of any kind). What is very interesting in two dimensions is that this appears to happen in two stages. First the solid loses its positional order, then it loses it's orientational order as well. This is vividly demonstrated in Fig 3. of the paper. The phase in the middle, with quasi-long range orientational order but short range positional order, is known as the hexatic phase.

When the lattice is shifted a bit the orientation can be maintained but the positions become disordered.