Past Projects

Using next generation computers and algorithms for modelling the dynamics of large biomolecular systems
Supervisor: Dr. Dmitry Nerukh

One of the main challenges in simulation of complex molecular processes such as protein folding or ligand-protein binding is the modelling of water: behaving as a structureless continuum in the bulk it needs to be represented at the atomistic level in a relatively small ‘core’ area of the system. The simulation of atomistic (explicit) water takes up to 90% of computing resources and makes the calculation prohibitively expensive. It is intuitively clear that the atomistic details are unnecessary in the areas distant from the biomolecule. However, in the vicinity of the biomolecule some water molecules are known to contribute to the biomolecular process in a very non-trivial way and their explicit modelling is decisively important.  The most natural representation of water in the bulk is provided by continuum hydrodynamics (CH).  Computer modelling in both representations, MD and CH, is well developed, but separated by a gap in the time and space scales accessible to simulations. Closing this gap is only possible if two directions are developed coherently: 1) new generation hardware, currently approaching the CH scales in MD simulations and 2) theory and software correctly joining the MD and CH representations.

The aims of this project are: to develop a new efficient theoretical and computational framework for hybrid MD-CH simulation of bio-chemically important processes at realistic time and space scales; to implement and test this framework in the world fastest supercomputing facility; and to conduct large scale simulations of trimethoprim (TMP) binding to dihydrofolate reductase (DHFR) and compare the predicted kinetic properties, the binding rate, with measured experimental values.

The project is a well balanced combination of state of the art computer hardware development, advanced numerical modelling (the triad of molecular dynamics, continuum fluid mechanics, and numerical methods) and cutting edge investigation of a biomedically important molecular system. For further information, see the project details here.

View some of our other past projects using the links below:

Islands of equilibrium
Inference Beyond the Limits
Composite Systems
Noise Computation