Grant: EWR Steacie Fellowships - Supplement

Biomolecules, such as proteins, DNA, lipids, and carbohydrates, exist in a microscopic universe with time and length scales 6-12 orders of magnitude smaller than the meters and seconds in which we measure length and time. They move rapidly on a time scale of nanoseconds and interact with individual water molecules the size of a few tenths of a nanometer. Most biomolecules are very small compared to the wavelength of visible light. This means they cannot be seen with ordinary microscopes, although there are many sophisticated experimental methods to measure aspects of the behaviour, shape, and interactions of biomolecules. Computer modeling is a complimentary approach to such experiments. Using powerful computers and a description of how atoms interact with each other, it is possible to calculate in atomic detail how lipids, water and proteins move and interact in time. In recent years, this molecular dynamics simulation method has been a very powerful method to solve problems involving molecules of all types, including biomolecules. This research project is aimed at developing and improving a computational model of molecules at a level of detail that is one level coarser than individual atoms. We group together about 4 atoms in a single 'bead'. By looking at the average interactions of such groups of atoms, we create a 'coarse grained' molecular model. Although we lose detail, it is computational cheaper by several orders of magnitude to explore such models. Many phenomena of biological or material science relevance are very well described by this level of detail. This project focuses specifically on improving the accuracy of our description of peptides and proteins. If we are successful, we will be able in the future to understand the molecular basis of new antimicrobial agents, the aggregation of proteins and peptides and their interactions with cell membranes and other biomolecules, and design new biocompatible materials for bioengineering purposes.