Computer Simulations of Biological Macromolecules: Seminar

Dr Sarah Harris, University of Leeds

Computational models have huge potential to provide insight into molecular biology by providing detailed animations of biomolecules and their interactions. Molecular simulation can show not only how the shapes of biomolecules change due to their thermal motion, but also how the structure of individual biomolecules is affected by subjecting them to mechanical stress. We use atomistic molecular dynamics simulation to investigate the structural and dynamic implications of DNA packing through supercoiling, and have shown that sufficiently high levels of torsional stress can induce structural transitions in DNA that may be of biological relevance. We have also developed a new algorithm that uses continuum mechanics to model biomolecules that are too large to be simulated at the atomisic level. These calculations emphasise the importance of dynamics, defects and disorder in biomolecules to our understanding of their mechanism of action in vivo.