Hello! I am a computational biophysicist specialised in developing minimal and coarse-grained models for biomolecules. During my PhD I worked on Fluctuating Finite Element Analysis, and I'm currently working in the Collepardo Lab at Cambridge on phase separation of Chromatin. 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.
KOBRA: Fluctuating Elastic Rods for Slender Biological Macromolecules
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.