I was pleased to receive an email from the Soft Matter journal that our recent article has become eligible for open access. This seems to be due to a new agreement that I guess might be specific to certain universities and/or funding sources. Anyway, we aren’t complaining! Now or in the near future our article on lipid bilayer domains will be open access.
Next week is the annual ACS Colloid and Surface Science Symposium — last year’s was very good and this one looks like it will be too. Hopefully there is as much good ramen in Pittsburgh as there was in Philadelphia. I’ll be giving two talks, both on the Tuesday. The first concerns methods for predicting and characterising the influence of polydispersity on a phase-separating fluid (with Mike Evans):
The second is about some more recent work on lipid bilayers, specifically how domain formation couples to asymmetry between the leaflets (with Peter Olmsted):
A few of us from Georgetown’s Institute for Soft Matter will be there, and I’m also looking forward to catching up with Ian Williams (he of the amazing colloidal corral). See you there!
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.
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.
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.
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.
Here’s a quick post about a couple of oddities and problems I encountered recently in Inkscape and Grace (on a Mac) in using them for preparing scientific plots. This kind of stuff isn’t especially well-documented online — it seems like people using these programs for this purpose often figure out a way that works for them and keep quiet about it. Also Grace in particular isn’t being developed at too fast a pace right now. Here we go:
- Exporting an EPS (or PDF or SVG) from Grace and then importing the file into Inkscape results in the fonts being changed from Times (Grace’s default) to some horrible sans-serif font in Inkscape, and the spacing being all screwed up. As explained and solved here (in relation to Matlab) this happens because Inkscape can’t access the Times font used by Grace (although weirdly it knows `Times New Roman’ which looks the same). So when it looks for the font referred to in the PDF you imported from Grace, it can’t find it, and just fudges it. Using Fondu to create a version of Times that Inkscape can use solves the issue.
- On Mac OS X Mavericks, installing Grace either via MacPorts or from source results in a couple of problems. 1) Thanks to updated Xcode tools, invalid arguments passed to the compiler generate an error not a warning and compile can fail. Apparently you can get around this by setting an environment variable, but it didn’t work for me. In Grace the problem is an `-m486′ flag which is passed to the compiler. I opened the configure script for Grace (or in MacPorts, the associated Portfile) and removed all mention of -m486 to stop this happening. 2) Once compiled, Grace on Mavericks seems to get a segmentation fault and crash on opening. This can be fixed in a hacky way by altering all mentions of the optimisation -O2 in the configure script to -O1. Or replacing a library helps to solve it properly, but I haven’t got round to that yet.
- In Inkscape, copy and duplicate are different. If you create nice clean text or a nice clean line or circle etc, and then ctrl-c ctrl-v like usual, the pasted object no longer seems to be like a vector and will be fuzzy when you zoom in. I’ve no idea why this is but I’m sure there’s a good reason. Anyway, using ctrl-d to duplicate instead preserves the nice vectory sharpness of the original object. Given the amount of copying and pasting that goes on in making my scientific diagrams, this was quite important to find out. This seems to make it more difficult to copy an object between different files, since ctrl-c ctrl-v works (but looks crap) whereas I can’t currently find out how to `duplicate’ an object between files.
- On opening an EPS or PDF you made with Inkscape at a later date in Inkscape, you may find that all the separate objects you had before behave as one object so it’s hard to remove or alter individual ones. You might end up using a nasty solution like a plain white box to block out bits you want to delete but can’t. This doesn’t seem to happen Inkscape’s native SVG format. If for whatever reason you don’t have the original SVG, sometimes it’s possible to select the single object in the imported EPS and then click `Object->Ungroup’. You can do this a few times to try and separate the different elements so they can be accessed one at a time. This is useful if e.g. you want to alter a figure somehow and don’t have the SVG.
I’m sure there will be experts who know more about these various issues — I’d be grateful for any more light shed. But hopefully someone who is experiencing any of these problems might find these quick and dirty solutions helpful sometime.
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.