Computer simulations of lipids

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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, both by themselves and in direct combination with experiments that otherwise could not be interpreted at a molecular level.***Using powerful computers and a description of how atoms interact with each other, it is possible to calculate in atomic detail how biomolecules move and interact in time. In recent years, this molecular dynamics simulation method has become an essential method to solve problems involving molecules of all types, in my research group primarily lipids. ***Lipids are the major building block of cell membranes that define the boundary between a cell and its surroundings. Cell membranes have remarkable mechanical and electrical properties, a complex chemical composition, and a surprisingly complex physical behaviour. These properties are primarily derived from the molecular structure of lipids, which have a water-loving head and a water-avoiding tail. This structure leads to self-aggregation in water into fascinating structures. These include cell membranes based on biological lipids, but also a wide variety of other structures by synthetic lipids and lipid mixtures, which are both of fundamental interest and of interest in technical and scientific applications. ***This research project is aimed at developing and applying computational models of molecules to better understand the properties of lipids and surfactant molecules. We will use and improve both detailed atomistic models and a somewhat coarser model in which a few atoms are grouped into a single 'bead'. Although we lose detail in this case, it is computational cheaper by several orders of magnitude to explore such models. Our main interests are the properties of domains in membranes, which are thought to underly many biologically important processes, the properties of mixtures of surfactants and lipids that form micelles, bicelles, and nanodiscs, and an improved link with experimental methods that give insight in lipid structure, including x-ray and neutron diffraction as well as spectroscopic methods. **