Research publication: Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics

At last year’s Biophysical Society 2015 meeting, Peter Olmsted and I met Philip Fowler, who at the time worked in Mark Sansom‘s group (he now works in the Nuffield Department of Medicine at Oxford). I had noticed a signal in their lipid bilayer simulations that looked like a two-step asymmetry/symmetry transition we had studied theoretically. Understanding how constituents of a lipid bilayer interact and self-organise is key to the biology of the cell membrane, as well as to applications of synthetic lipid bilayer membranes.

It has been a pleasure to work with Phil and Mark over the past year as we have looked closely into the symmetry and asymmetry of phase-separating bilayers, using a raft (geddit?) of new simulations expertly constructed and analysed by Phil. A joint paper is out now in JACS, linking the kinetics of lipid bilayer phases to a theoretical model of competing inter-leaflet coupling effects. Check it out!

Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics

An achemso.bst LaTeX bibliography style modified to display first page only

I was recently preparing a paper for an ACS journal and had a few issues with the bibliography style. Most of these were fixed by downloading the latest achemso.bst style file from here. However, it didn’t include that the journal seems to use only first pages (not ranges) when making references. That is, an article on pages 1897–1902 is referred to as:

Authors, Journal, Year, Volume, 1897

and not:

Authors, Journal, Year, Volume, 1897–1902.

So, using some information from here I have made a modified achemso.bst that uses only the first page. I don’t know about you but it always takes lot googling to figure out this stuff, so I’ve tried to make this post easily findable by those in a similar situation.

Update: kinetic Monte Carlo simulation code example

I had an old blog post linking to a walkthrough of the code developed and used during my PhD on phase separation of polydisperse colloids. It’s now a little deprecated, partly because I’ve done further work on that topic since then, and because a link it contained had become dead.

Now, here is a short post to provide a quick-and-dirty runnable example of the latest code. I’ll provide a link to the repository, and then mention a new EXAMPLE folder which contains a minimal working simulation setup. Finally I’ll briefly overview what the code and analysis tools can do.

Repository: https://bitbucket.org/johnjosephwilliamson/phd-code-clone-bitbucket

EXAMPLE folder:

Screen Shot 2016-04-15 at 15.54.48

  • The README.txt contains instructions
  • preinit.txt controls the initialiser program, which is run in order to pack the simulation box with particles of the required volume fraction, polydispersity… This file is set to make a simple cubic box (XLATTICE 0 etc.), without the fancy crystal templating algorithm we used in some applications
  • simconfig.txt controls the main simulation, and in this case is set to simulate hard spheres (DEPTH and RANGE of square wells is set to 0)
  • The other files are binaries to be run from the command line, which I suppose might run as is if you have a mac configured similarly to mine. Else, they can be compiled from the source code in the repository. The appropriate source code folders are mentioned in the README. In the top-level-directory of the repository, there is another README which provides compilation flags (linking to “math” and “boost” libraries) which may be necessary, but for me on this computer were not
  • XYZ_converter allows converting the output to .xyz format for visualisation in OVITO
  • Profit…

Screen Shot 2016-04-15 at 16.04.19

Conclusion:

Naturally, let me know if you have any trouble compiling or running the code. See my publications page for examples of what we have done with it. If you are interested in using or adapting the code, I am always happy to explain it in more detail. Briefly, the existing capabilities/purposes:

  • kinetic Monte Carlo simulation of noninteracting, hard-sphere or square-well colloidal particles
  • Gaussian or Schulz polydispersity, with two choices of how the square well polydispersity relates to the hard-core polydispersity
  • geared toward study phase-separation kinetics in polydisperse systems, local characterisation and structural information
  • isotropic simulation box, or a special cuboidal geometry in which a crystal is templated at one end (choice of two crystal faces), to study crystal growth kinetics
  • XYZ_converter to produce standard .xyz files, for OVITO visualisation
  • a wide suite of analysis programs: structure factors (including intermediate scattering functions and partial versions thereof for polydisperse cases), polydisperse fractionation measurement, coarse-grained-Voronoi local volume fraction analysis, crystal interface-tracking, kymographs…

 

 

New job

I recently left Peter Olmsted’s group in Georgetown after a very enjoyable two years. We studied the phase separation kinetics of mixed lipid bilayers, specifically the effects of inter-leaflet coupling. The Institute for Soft Matter Synthesis and Metrology is a very pleasant and stimulating place to work, and I strongly recommend it.

In the past week I’ve moved to become a postdoc in the group of Guillaume Salbreux at London’s new Francis Crick Institute. The work will concern the mechanics of tissue development and homeostasis, in close collaboration with some excellent experimentalists. The move from a sort of “physical chemistry of lipid membranes” to a more explicitly biological “physics of living systems” seems a natural step to make, and I’m looking forward to the next few years of research.

In the meantime, check out the latest paper with Peter (a comment in PRL), and look out for an upcoming collaboration with Philip Fowler.

Research publication: Kinetics of symmetry and asymmetry in a phase-separating bilayer membrane

A new paper with Peter Olmsted has just appeared in Physical Review E. Like our recent Soft Matter article, it builds on our theoretical study of coupled lipid bilayer leaflets, investigating the underlying model via direct simulation. We also give a broader look at the use of “leaflet-leaflet” phase diagrams, introduced in previous theoretical works, which allow a more natural interpretation of symmetry and asymmetry in bilayers.

Open access: Nucleation of symmetric domains in the coupled leaflets of a bilayer

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.