Chemistry and Materials Earth Sciences and Environment Engineering and Energy Fundamental physics Mathematics and Computer Science Medicine and Life Sciences All 
Coupling Across the Continuum-Particle Divide with Code_Saturne and GROMACS
ARCHER2-eCSE08-11 : Dr James Gebbie-Rayet (STFC Daresbury Laboratory)Subject Area:
Medicine and Life Sciences As research in the life sciences tackles increasingly complex problems, simulation is becoming ever more important. Biomolecular simulation often involves multi-scale modelling, where different methodologies are used to carry out macro-scale and micro-scale simulations. These are then coupled so that information can be exchanged between the different scales. However, multi-scale modelling approaches have previously been limited in terms of the range of scales and applications that they can address. This eCSE project has enabled simulations of large complex biological systems in a way that was not previously possible, by coupling a continuum physics code (Code_Saturne-CDO), which simulates protein evolution at the macro-scale, with a particle-based physics code (GROMACS), which handles the potential binding / repulsion at the micro-scale. By coupling these two methods, information can be exchanged between the scales to decide which action (binding/sticking or repulsion) follows. Generalising this investigation to many proteins (at least several hundred thousand within a single cell) can only be achieved using High Performance Computing (HPC). Results show the coupling implemented in the project to be very efficient. Read more...