🎄12 Days of HPC 2021

Festive Tension

Blog post number 14 in our 12 days of HPC series from Faculty of Biological Sciences!

During the month of December we’re featuring blog posts from researchers from across the University of Leeds showcasing the fantastic work they do using our High Performance Computing system. Follow us @RC_at_Leeds to keep up to date with our 12 days of HPC blog series.

What’s your name?

Alexandra Holmes

What department do you work in?

Faculty of Biological Sciences

What research question are you trying to answer?

I’m trying to work out how a protein called Piezo1 works. Piezo1 is a mechanosensitive ion channel - which is a fancy way of saying it is able to tell when there is pressure on a cell and pass charged particles through itself in response. A bit like that one member of your family that can tell when an argument is brewing round the dinner table and reacts by bringing out a cheeseboard to distract everyone. Just like us mere mortals that wish we knew how that relative knows the game of charades is about to dissolve into chaos, I’m wanting to find out how Piezo1 senses tension and how it mounts a response.

What tools or technologies do you use in your research? (Programming languages, packages, APIs)

I mostly use Gromacs - a molecular dynamics simulation software, python, and others

How does HPC help your research?

Piezo1 is large - think just eaten a whole Christmas dinner, with trimmings, large. Being big means there’s plenty of atoms I need to work with, and that’s just impossible to do on a normal computer so that’s where HPC steps in to supercharge my simulations and get them done in a reasonable time scale so I can finish my PhD at some point this decade (and stop the distant family members from asking when I’ll be graduating).

What is the potential impact of your research?

Proteins like Piezo1 are the “business end of biology”. Everything you’re doing right now involves them, so understanding how they work is fundamental to understanding life itself (or that’s what I tell myself to get my motivation up when I generate yet another error message). Piezo1 in particular is a hot topic at the moment, it was recognised in the 2021 Nobel Prize, so it’s of particular interest to work out how it does its job!

In your personal opinion what’s the coolest thing about your research?

Honestly? This is an awful answer for someone who wants to make science accessible and knows you don’t need to use niche scientific words to get points across, but do you know how cool it is to say “yeah let me just adjust the forcefield and then we’ll get this up and running on the supercomputer”? yeah getting to say some absurdly sci-fi-esque phrases it a pretty cool thing to do in your day job!

In your opinion, what is the ultimate Christmas song?

The Eartha Kitt version of Santa Baby - I too would like a yacht and a platinum mine this year

piezo1 xmas tree - a stack of upside down Piezo1 structures arranged into a Christmas tree shape.