Gone imagin’

Recently I’ve been behaving more like an intern at Pixar than a scientist — yes, it’s time for some scientific imaging. In my field of simulation/theory, some form of imaging is important in a prosaic kind of way in order to get a feel for what is going on, and check for any disastrous bugs. But it’s more and more becoming a real mode of scientific communication. Journal covers commonly feature either simulation renderings or even schematic artists’ impressions, as well as the more traditional fare of, e.g., beautiful images from a microscopy experiment. 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.
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