Nothing stays still. Even at the atomic level – especially
at the atomic level – forces between particles keep them wriggling, even when locked in a relatively 'stable' structure. In these computer simulations, researchers mimic tiny proteins in the conical outer shell or capsid
of the human immunodeficiency virus
. Each pentamer (green) or hexamer (cream) structure is built from smaller building blocks called monomers – the model traces their jostling movements over nanoseconds. Simulating so many moving parts at once is a huge challenge for computer power, so the research team uses new methods to balance the ‘granularity
’ of the model – how abstracted the molecular details are from real life – with how faithfully they mimic the overall biological behaviour. New algorithms using a 'coarser' granularity require less computer power (and energy), opening up the power similar simulations to more research groups worldwide.
Written by John Ankers
A former researcher in systems biology, John is now an online biology tutor and professional coach supporting the wellbeing of scientists and NHS professionals. He's writing, too, of course.