A week ago I took a quartet to Inkwell Arts in Leeds to perform some of my favourite standard and less-standard tunes, along with some arrangements from Vangelis’ wonderful jazz-noir soundtrack to Blade Runner. Ex-Leeds saxophonist Matt Anderson and Leeds-based smashers Martin Longhawn (keys) and Steve (‘Chief’) Hanley (drums) joined me. It’s quite a privilege to have these great musicians and old friends play your charts and seem to enjoy doing so :-).

Anyway, we were fortunate to have Chris Milnes there taking a few videos and sound recordings, so I’ll be uploading some over the coming weeks. Here’ s an extract from Lee Konitz’s line It’s You (over It’s You or No-One). The full video link is at the bottom.

Full video

In Washington DC I had the pleasure to meet and play with lots of amazing people. Perhaps the highest joy was meeting Brad Linde and Billy Wolfe at a big band gig in my first few weeks, and joining their avant-garde/americana project along with super-hip New York cats Aaron Quinn and Deric Dickens. (I also eventually joined the wonderful Bohemian Caverns Jazz Orchestra, which Brad leads with Joe Herrera.) We’ve released our second album and I just got round to making this trailer with a few extracts.

I tried to be representative, so there’s a bit of Haskell’s beautiful Starlight, Billy’s quasi-Konitzian original Turkey, Deric’s lilting and folky Pickett Fence, the standard Meet Me Tonight In Dreamland, and Aaron’s terrifying (which can be oiled in different patterns for different techniques). Finally, the video ends how the album begins, with Brad counting off a free blow named Gotta Blast!

Check out more and buy it here.

Here’s a rough transcription of Steve Swallow, one my favourite bassists, playing on the album Three Guys with Lee Konitz and Paul Motian. (Dreamy band or what?). It’s a Konitz composition over It’s You Or No One. So far, I can’t find it online (a tiny sample in this article) but I’m reliably informed it exists on somewhere on youtube.

Anyway, here is the unison line that ends the tune:

It’s You unison line transcription

It’s You unison line (Eb)

And here it is played in somewhat Swallow-y style — very light roundwounds with a pick and loads of tone rolled off:

Connoisseurs will know that the pick should really be copper, and the bass a semi-acoustic with a piezo somewhere, strung E-C, etc.

I’m really interested in the relationship between the arts and sciences (see, e.g., here), and today a few of us from the Crick Institute received a guided tour of a nice exhibition at Central Saint Martins. Crossing Fields is the degree show for their almost-unique MA in Art and Science, and is well worth a look in the next few days. A few that I managed to get snaps of are shown below — there are many more fantastic works to see. These ones are by Julie Light, Meri Lahti and Chang Zhou.

IMG_7164IMG_7156IMG_7158

You don’t need to be a biologist to work at the Crick Institute! I’m not. If you are an undergraduate, here’s a way to sample the life of a biological physicist…

As an undergraduate, I hadn’t considered working in research until I fell into a summer research project with the excellent Mike Evans at Leeds. He actually ended up being my PhD supervisor, but in a broader sense the placement opened my eyes to the process of doing “new stuff”; the feeling that what you’re doing hasn’t been done before is quite a special one.

Anyway, this year I’m part of the Crick’s summer student programme, and have a project open on applying quantitative and physical principles to a biological system. Details can be found here.

 

 

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

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 [link fixed 24/7/18] 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.

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…

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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…