🎄12 Days of HPC 2022

Bacterial Christmas Cake

Blog post number 10 in our 12 days of HPC series from School of Computing!

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?

David Head

What department do you work in?

School of Computing

What research question are you trying to answer?

The role of dietary sugars on the evolution of the dental plaque biofilm, and how this may trigger a ‘transition point’ from healthy plaque (which is a thing), to unhealthy plaque (‘symbiotic’), that is predicted to convert sufficient sugars to acids so as to demineralise tooth enamel, otherwise known as tooth decay.

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

Intel C++11 compiler

How does HPC help your research?

Being able to run multiple high-fidelity bacterial simulations simultaneously, each requiring 4-8 cores, allows the parameter space (which is vast, for biological problems such as this) to be sampled within a reasonable time frame that would not be possible with cluster resources.

What is the potential impact of your research?

We have used the simulation findings to test hypotheses for the relationship between dietary sugars and oral health, and used this to highlight oral health regime changes and/or therapeutic products most likely to improve oral health.

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

Collaborating with microbiologist and clinicians to produce simulations with the potential for genuine impact in the application domain.

Postscript

Collaboration with Livia Tenuta (Michigan), Phil Marsh and Deirdre Devine (both School of Dentistry, Leeds).

Orange and green balls stacked under a white tooth simulating dental plaque aggreation — This shows a snapshot of a simulation of dental plaque after 50 days of pulsing sugar into the system. The upper white 'slab' represents the tooth surface (the RGB values match those for tooth enamel), and the balls below correspond to bacterial aggregates, consisting of two types - 'good' bacteria (that do not produce much acid) in green, and 'bad' bacteria (that can produce sufficient acids to cause tooth decay) in red. This example corresponds to a borderline case in which the frequency of sugar in the diet lies right at the 'tipping point' between healthy (all green) and unhealthy (all red) plaque.