Biological macromolecules such as proteins and nucleic acids consist of thousands of atoms. Whereas crystallographic data of these molecules provide baseline information on their three-dimensional structure, their biological function can depend to a great extent on mechanical characteristics such as conformational flexibility. In this course, we will examine numerical methods for modeling shape fluctuations in large biomolecules using coarse-grained elastic network models based on foundations of engineering structural dynamics. The course will consist of attending lectures, reading papers, and performing computer projects. No prior knowledge of biochemistry or molecular biology is required.
Knowledge of linear algebra and differential equations. Basic knowledge of Newtonian and Lagrangian dynamics will be helpful, but these will be reviewed.