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This class will provide an overview of methods for molecular simulation of biomolecules and membranes. We will study methods for atomic detail molecular dynamics and Monte Carlo simulations. After discussing basic algorithms such as integrators, thermostats, and barostats, we will study how biomolecules are chemically parameterized to accurately capture their conformational equilibria. This knowledge will then be used to build, simulate, and analyse a molecular model of a membrane protein embedded in a lipid bilayer. The simulation will be used to understand how these methods can be used to obtain insights into the molecular mechanisms of protein function.