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!
My research interests include kirchoff rods, molecular dynamics, and coarse-grained simulations at the molecular mesoscale. I have experience in high-performance computing, development and design of simulations, molecular dynamics, mathematical logic, computational biophysics, photonics and optics, and statistical mechanics.
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.
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.
As you probably know, halogen light bulbs are incandescent: they produce light as a side effect of being heated up. Conversely, LEDs are semiconductor devices, and prolonged heat can be very damaging to them. LED devices tend to be cooled in a similar way to computer CPUs - using a thermal interface (like thermal paste) a heatsink, and sometimes a fan as well. However, the effectiveness of these cooling methods can vary wildly, depending on the operational limits of the LED and the type of thermal interface being used. In this article, I'll discuss the experimental methods I designed to characterise the thermal performance of LEDs using a variety of cooling methods.
The Bohr Magneton is a physical constant which is used to express the dipole moment of electrons. It corresponds to the angular momentum of an electron in the lowest orbital. The Bohr Magneton relates the splitting of atomic energy levels to the strength of an applied magnetic field. The Zeeman effect offers us an easy way to observe this splitting. In this lab report, I discuss a how to observe the Zeeman effect, and how it can be used to compute an accurate value for the Bohr Magneton.
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.