Category Archives: Computing

Membrane biophysics

I very recently completed a PhD with the truly excellent Mike Evans. As detailed on my science page we were working on model colloidal systems to study some general features of phase transitions (gas-liquid, crystal-fluid, etc.) particularly in polydisperse substances — where every particle is slightly different to every other. The work produced some interesting results and nice publications with more to come, and culminated in this hefty tome.

I’ll now be staying at Leeds for the next couple of years, but my day-to-day work (i.e. funding) concerns a new topic: the biophysics of lipid membranes. Yes, having spent over 3 years figuring out how to explain to people what I do, I now have to start from scratch. It seems like a good time for a quick post explaining the topic, and what attracted me to it.

Cells and life

How did life begin? Of course, nobody knows precisely. However, we can speculate reasonably on what the earliest life was like. It is overwhelmingly likely that the first things in any sense ‘alive’ were tiny protobacterial cells, roughly spherical containers of stuff with little internal structure which, agonisingly slowly, acquired the capabilities we associate with life: reacting to their environment, duplicating themselves, and so on. A nice paper by a collaborator of mine discusses (Section 2.1) the characteristics of the first life, and reasons why the simplest — earliest — possible life probably must have inhabited the length scale we associate with simple bacteria.

One of the criteria for life is particularly simple and, to me, quite satisfying, because it seems to spring from simple logic rather than particular accidental features of our world. A living thing in the sense we understand it should have a boundary which distinguishes it from its environment. Where does the outside end and the organism begin? The other criteria for life — reproduction, motility, response to environment etc. etc. — rely on there being an answer to this question. Intimately related to this is the idea that something living should be able, to any extent, to regulate its internal chemistry, distinct from changes in its environment. If we, humans, simply filled with seawater when entering the ocean; or if our organs were not contained ‘inside us’ but just wandered around the universe independently, we’d have a hard time proving ourselves to be alive. Similarly, the cell’s boundary couldn’t just be a fully permeable, abstract dividing line which allowed the cell interior to remain in permanent, passive equilibrium with the outside world. So, cells specifically and life generally must be able to selectively exchange chemicals with the outside world. Hopefully, my point is coming into view. A cell boundary is key to life not just as a logical prerequisite for even speaking about life as we know it, but as the focal point for the very processes that render the cell alive: its interactions with its environment.

Lipid membranes

In living cells, ‘lipid membranes’ serve to encase the cell and to mediate exchange with the environment. What are they? For a physicist, a lipid is most instructively thought of as being a tadpole-like molecule. The ‘head’ likes water — it is hydrophilic, because it is polar and therefore doesn’t too much disrupt water’s hydrogen-bonding network — while the ‘tails’ don’t like water, being nonpolar and therefore hydrophobic for the same reason that everyday oils are. Allowing a whole bunch of these lipids to undergo thermal motion in a watery solvent results in arrangements which keep the water-hating tails as far as possible from the water, shielded by the heads. See this picture. The lipid bilayer arrangement is a roughly flat sheet which can fold up to make a roughly spherical vesicle (i.e. a structure appropriate to form a cell).

The lipid membrane mediates a huge variety of vital processes: cell division requires the spherical membrane to form a ‘bud’ which eventually breaks off; selective exchange of ions and other important things takes place through ion-channel proteins embedded in the membrane; inter-cell signalling and detection processes necessarily take place through the membrane; the list goes on.

Understanding how lipid bilayers work involves a heavy physics component, to understand properties such as membrane curvature, asymmetry (one layer being different from the other), phase separation, formation and break-up, and the interdependence of these properties. The CAPITALS programme is a large collaborative project aimed at this target, and my new work is part of it. The people in charge (principal investigators) are real experts in the field, and everyone involved is extremely switched-on and open-minded — it’s great to be part of it.

Here’s a snapshot from some early computer simulation work I’ve been doing. It’s a homemade version of a wide class of models where simplified lipids are represented as chains of 3 beads, one hydrophilic (green) one and two hydrophobic (red) ones.

3bead_lipid_model

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!

 

Fluid simulation code walkthrough

As part of coming to the end of my PhD project, I need to leave the computer simulation code I’ve written (a Kinetic Monte Carlo algorithm for square-well/hard sphere particles) in a state which at least theoretically allows it to be used by someone else. So, I’ve written a brief manual/walkthrough (below) which contains just the detail needed to run a simple simulation of gas-liquid separation.

simulation_manual (click to download)

Requirements:

  • A Mac, ideally, with a C/C++ compiler installed (I use gcc — from within Xcode preferences, install the command-line tools).
  • Basic familiarity with the Mac terminal.
  • OVITO for making pictures/videos of the simulation, which is the best bit.

The manual completely walks through downloading, building, running and visualising the simulation, and might be a nice way to spend half an hour. Enjoy!

Research paper: The effects of polydispersity and metastability on crystal growth

I’ve just uploaded a preprint of a new paper me and my supervisor are writing to arXiv. It’s a freely-available repository research in loads of different areas which people use to make research available before and while its in peer review for a journal.

This one is to do with crystal growth in soft condensed matter. That includes colloidal crystals and closely related things such as proteins, which must be crystallised in order to study their structure in biological/medical research. The broad question of ‘What’s the best way to grow a crystal?’ is relevant in a lot of scenarios, especially given that one is often quite free to vary the conditions in the system to optimise growth; for instance the interactions in a e.g. colloidal suspension can be easily tuned by adding other species such as polymer coils into the solution.

The dynamics of phase transitions, i.e. how systems do or do not actually reach their true equilibrium state, is an important consideration in applying thermodynamics to soft matter. In this paper, we simulate crystal growth (as shown in the video here) in the presence of metastable gas-liquid separation, which may be encouraged or avoided by tuning the interaction potential in a system, and polydispersity, which usually cannot be avoided in soft matter. There’s a variety of nice visualisations showing the effects of these two factors on the crystal growth dynamics, and we find that they can interact in a complex and previously unknown way. The simulation findings are related to existing experimental data and to theoretical considerations. Here’s the link:

The effect of metastability and polydispersity on crystal growth kinetics

This work, in early form, was the subject of a recent internal seminar in the Soft Matter Group at Leeds. I’ve uploaded the slides and an audio recording from the seminar.

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.

A science picture

Click the photo for a high-res version

Here is a photo I recently took with my friend Tom. It’s a little tube containing a suspension of colloidal particles (described a bit more on my Science page). Colloids are small but not microscopically tiny, which means that when they form crystals, the typical distances between particles are larger than those found in molecular or atomic structures. In fact, the distances correspond roughly with the wavelength of visible light, so the crystals scatter incoming light of all different colours and, as shown in the picture, look great. Natural and synthetic opals also display this ‘opalescence’, because they are formed by the crystallisation of colloidal sand particles.

I got this little sample when I was on a conference in Corsica and I’m very fond of it, because the only colloidal suspensions I usually get to see are pretend ones in computer simulations. The motivation for having spent a morning with Tom pointing a camera at a tube is, hopefully, to provide a nice green-screen background for an interview I was involved in for the Physics Department’s website. In the interview I managed to talk for 15 minutes about why Leeds is a good place to do a PhD, while forgetting to once mention its music scene. Well done me.

Thanks very much to Tom West for his incredibly steady camera-hands, and patience.

Jerusalem and Audio Hijack Pro

I’ve just updated my music page with a recent arrangement of Elgar/Parry’s lovely socialist hymn, ‘Jerusalem’. This somewhat confused adaptation was part of a last minute effort by Steve Wright and myself to provide patriotic material for one of the gigs on LUU Dance Band’s 2011 tour of France — the gig happened to fall on St George’s Day, so the enthusiastic and numerous ex-pat community of Bergerac had requested that Jerusalem and Land of Hope and Glory be played that night. We forgot about it until a week before the tour, during which Steve was very busy with other things, and fun ensued.

I hope soon to upload an export or recording of Steve’s wonderful jazz-waltz setting (yes) of the latter tune, but for now here is an export of Jerusalem using the Sibelius 7 Sounds library.

Due to a minor bug and the fact that it was made in Sibelius 6 originally (I think), the inbuilt export chopped off a few notes, so I used the terrifying and excellent Audio Hijack Pro, a great Mac application that is able to steal the audio from any program and record it to a file.

TotalTerminal for Mac OS X

Quite a few people I know who use a Mac like to take advantage of the UNIX-like Terminal from time to time. I use it for remote logins to the computer clusters that do my PhD work for me, but there are all sorts things you can do using the built-in command line utilities, and for certain automated or repetitive tasks it’s often far quicker than using a graphical interface.

I recently found a great application called TotalTerminal which takes control of OS X’s inbuilt Terminal app and allows it to bring up a terminal ‘visor’ just by pressing a shortcut, a bit like the console in iD Software games like Quake, Doom etc. This is very handy if you want quick access to the command line regardless of what else you’re doing at the time, and it’s very customisable too. I use ‘Apple+§’ to bring up a terminal from the bottom of the screen, so that I can quickly use SSH to check on my simulations.