Integrating Biological Simulations
1st March 2006 to 28th February 2008
The overall aim of this project is to explore and establish an integrated approach to computational systems biology spanning from the chemical to the subcellular level of simulations. Biomolecular simulations play a key role in enabling us to study and understand biological processes at a microscopic level, not always accessible to experiment. Thus simulations are essential for interpretation and extension of experimental information, and are becoming increasingly important as methods and computer technology advance. Biomolecular simulations are also a key element of a genuine predictive biology, enabling us to employ the results of structural biology in a non-reductionist fashion. However, no single method can achieve all the levels of detail needed. Hence, we wish to integrate simulations ranging in level from the mechanistic (i.e. bond breaking and making) through ligand-protein interactions and conformational changes to ligand diffusion in a membrane. In the course of these studies we will exploit the biological usefulness of this approach, and will develop the use of HPC in multi-level biomolecular simulations. This will have a strong multi-disciplinary element and will bring to biological modelling both e-Science and simulation techniques from the physical and computational sciences.