Hello! I am a computational biophysicist with experience in minimal method development, elastic rods, liquid-liquid phase separation, research software engineering and high-performance computing. Previous: FFEA Group at Leeds, Collepardo Lab at Cambridge. Current: computational scientist at the STFC. You can get in touch with me at [email protected]. While you're here, please take a look at my CV and LinkedIn profile!
I have been writing software for 12 years, mostly in C++ and Python. During this time, I’ve developed websites, games, graphical applications and number-crunching tools in a variety of languages. I’m also a bit of a Linux geek!
During 2021 I worked as a senior research software engineer on the MOLPRO, quantum chemistry package. This post details my work on optimising and profiling MOLPRO's linear algebra libraries, and the results.
KOBRA is a fluctuating Kirchoff elastic rod algorithm for performing dynamical simulations of slender biomolecules, such as alpha-helices and coiled-coils. It can support parameterisations of objects with arbitrary equilibrium shapes and inhomogeneous, anisotropic material parameters, and it can reach second-scale trajectories of quite large systems on modest workstation hardware. It's written in C++ and is released, for free, under the GPLv3 free software license. So far, KOBRA has been used to build models of Ndc80C, the SMC complex and Myosin-V, and may soon be deployed to study COVID-19 spike proteins. This page will contain links to the KOBRA publication, my PhD thesis, download links and installation instructions.
I had intended to give this presentation over the spring and summer of 2020, but I only got to give it once in person. It's a quick overview of the KOBRA algorithm and software, with some discussion of Ndc80c and the kinetochore.
I gave this presentation at the 2017 Visegrad Symposium at Nove Hrady, Czechia, and again in 2018 at the CompBioMed AHM. It's a quick overview of the FFEA algorithm and software package.
FFEA is a continuum mechanics biophysics simulation package designed for large, complex systems of biomolecules. It had been in use at Leeds for a few years (mostly for simulations of the motor protein Dynein), but now it's free software that anyone can download. In this article I'll talk about my work on the software so far and on the FFEA software publication in PLOS CompBio.
Tower of Solomon is a free couch multiplayer tower-climbing game for 2-4 players. Build blocks to climb the tower, and try to outlast the other players. If you die, you turn into a screaming skull, so don't do that. You can also find the game on my itch.io page.
That is the question. A look at using bleeding-edge simulation techniques to understand the inhibition behaviour of Myosin-VII. I gave this presentation as part of my undergraduate final project in early 2016. It’s aimed at people who are familiar with basic physics concepts, but not biology or biophysics. You can find more technical information about the project here.
Myosin-VII is part of the Myosin family of motor proteins. It has a key role in the operation of biological structures in the eye and inner ear. Unfortunately, the dynamics of Myosin-VII and its inhibition are poorly-understood. This article details my use of FFEA (Fluctuating Finite Element Analysis), a coarse-grained continuum simulation package, to model the motion of Myosin-VII, and understand its inhibition behaviour.
One of my responsibilities at Sharp was testing and analysing the type and quality of light produced by LED devices using an integrating sphere. I developed a graphical tool in Python that would automatically interpret spectral power distributions, read metadata from files, compute a large variety of colour metrics, and automatically generate PDF reports.
A random walk (sometimes called 'the drunkard's walk' describes the motion of a particle that undergoes a series of random steps. But what happens if that particle is a quantum particle? This article presents a few interesting ways of visualising this motion, using Python and matplotlib.