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:

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  • 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…

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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…

 

 

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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.

ACS Colloid and Surface Science Symposium 2015

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):

Talk 1

The second is about some more recent work on lipid bilayers, specifically how domain formation couples to asymmetry between the leaflets (with Peter Olmsted):

Talk 2

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!