New Publication: NRas slows the rate at which a model lipid bilayer phase separates

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Here we examine by computer simulation what effect adding a small cell-signalling protein does to a model ternary lipid mixture that has been shown before to phase separate. This paper was presented at the 169th Faraday Discussion meeting in Nottingham in May 2014, the theme of which was Molecular simulations and visualization. We followed the progress of the phase separation of the lipid bilayer by measuring the length of the interface using an edge detection algorithm from image processing. An example python script can be downloaded here.

We found that the protein, NRas, indeed slows down the rate at which the bilayer phase separates. The protein also tends to localise to the interface between the domains which is consistent with it acting to reduce the line tension between the phases.

The questions asked during the discussion (and my answers) will be posted on the journal’s website soon. I’ll update this post when that happens. This paper is open access so is free to download.

Trying to stop lectures from being so zzzz…

Why are lectures so sleep inducing? I remember well the effort required to keep your eyelids apart after 35-40 minutes. So, now that I am the lecturer, how can I keep my students at least awake, and hopefully interested? I am not going to talk about the most obvious point, which is to be an enthusiastic and engaging lecturer. Instead, I shall briefly list the tactics I am trying this year in my lecture series, which started this week.

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Rushing here and there: planning an itinerary for a large scientific meeting

sfI’ve just returned from the 58th annual meeting of the US Biophysical Society in San Francisco. With around 7,000 scientists, multiple simultaneous sessions of talks and nearly a thousand posters every day, it is a large event, but not as big as many. Even so, working out what talks and posters you might want to see is a difficult task. Of course, you might not wish to prepare a schedule as this is somewhat of a personal thing, but I find it helpful just to know how the days will ebb and flow – if today is busy, will tomorrow be a bit quieter and let me recover? If I bump into someone I want to talk to, what will I miss? What posters might be interesting on the other side of the exhibition hall? I emphasise that attending interesting talks and seeing posters are not the only things one does at these conferences – talking to people is useful and fun too – but having that side of it organised does, I find, take your mind off “the next thing”.

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GROMACS 4.6: Running on GPUs

fig-blog-gpu-1I mentioned before that I would write something on running GROMACS on GPUs. Let’s imagine we want to simulate a solvated lipid bilayer containing 6,000 lipids for 5 µs. The total number of MARTINI coarse-grained beads is around 137,000 and the box dimensions are roughly 42x42x11 nm. Although this is smaller than the benchmark we looked at last time, it is still a challenge to run on a workstation. To see this let’s consider running it on my MacPro using GROMACS 4.6.1. The machine is an early 2008 MacPro and has 2 Intel Xeons, each with 4 cores. Using 8 MPI processes gets me 132 ns/day, so I would have to wait 38 days for 5 µs. Too slow!

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The Oxford Software Carpentry Boot Camp … one year on.

In October 2012 I organised a Software Carpentry Boot Camp at the University of Oxford. I’ve previously posted the feedback I gathered immediately before and after the boot camp, but thought it would be interesting to see if all that enthusiasm actually translated into deeds i.e. did the attendees actually change how they worked as result of the boot camp? So almost exactly a year after the boot camp I sent around a similar survey to the attendees. Inevitably some email addresses were now invalid so I only received responses from 13 of the attendees (as compared to 25 immediately after the workshop). To encourage responses, I only asked three questions and two of these followed on from questions I had previously asked. So what did I find out?

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