PhD projects advertised
If you are interested in helping combat antibiotic resistance and want to work on an interdisciplinary computational project with the possibility of strong public engagement →
bashthebug.net alpha launch
I’m planning to launch a citizen science project, bashthebug.net, in 2017 which has two distinct ways anyone can help combat antibiotic resistance. I’ve revamped and relaunched what will ultimately become the public-facing project website – please have a look. The first strand is closer to the light of day and →
New Publication: Lipids can form anti-registered phases
When we think of lipids phase separating in a cell membrane we usually think of this process occurring symmetrically, i.e. with like on top of →
New Publication: Proteins Alter the Stiffness of Membranes
Although there have been many studies of proteins whose primary function is to ‘sculpt’ the surface of membranes e.g. BAR domains, there have been very →
New Publication: Membrane Compartmentalization Reduces the Mobility of Lipids.
Lipids are not free to diffuse around the cell membrane. Rather they are constrained not just by all the embedded proteins but also by the →
Cheltenham Science Festival
A bit over a week ago I helped run the Modernising Medical Microbiology stall at the Cheltenham Science Festival. This was my first time helping →
GROMACS in DOCKER: First Steps
DOCKER is cool. But what is it? From the DOCKER webpage Docker containers wrap up a piece of software in a complete filesystem that contains →
Setting up a GROMACS cluster
Recently I’ve moved to the John Radcliffe hospital and my old lab kindly let me have some old servers that were switched off. This pushed me to learn how to setup them up as a compute cluster with a scheduler for running GROMACS jobs. I’ve wanted to learn this for →
How to setup a Gramble
This is a Gramble, which of course is short for a GROMACS Bramble, or, in other words, a Raspberry Pi 2 model B cluster running GROMACS. Given the ARM processor in a Raspberry Pi 2 does not allow SIMD instructions like the more complex (and expensive) Intel chips, why would →
I’ve moved…
Today is my first day as a Senior Researcher in Modernising Medical Microbiology in the Nuffield Department of Medicine at the University of Oxford. Practically I’ll be based at the John Radcliffe Hospital in Oxford. I was a Postdoctoral Researcher in the SBCB Unit at the Department of Biochemistry for →
New Publication: Predicting affinities for peptide transporters
PepT1 is a nutrient transporter found in the cells that line your small intestine. It is not only responsible for the uptake of di- and tai-peptides, and therefore much of your dietary proteins, but also the uptake of most β-lactam antibiotics. This serendipity ensures that we can take (many of) →
GROMACS on AWS: compiling against CUDA
If you want to compile GROMACS to run on a GPU Amazon Web Services EC2 instance, please first read these instructions on how to compile →