Chem 396:
Molecular Modeling and Simulation
Prof. D. L. Beveridge, Chemistry Department
Tue (Lecture).Thur (Lab) 01:20PM-02:40PM; SCIE 72
“Modeling” is explicitly or implicitly involved in nearly every aspect of understanding complex molecular and macromolecular systems. Modeling takes a variety of forms in the chemical sciences, including conceptual, schematic, mathematical, and computational. The history of chemistry is deeply intertwined with the development of models such as Lewis structures and kinetic theory, which provide useful results involving only a few variables. However, most chemical systems of practical interest today involve the interplay of many variables, and computational models based on quantum mechanics, statistical mechanics, and chemical dynamics are required. Molecular Modeling and Simulation (MMS) considers the modeling paradigm applied to chemical systems, and introduces the computational methods in current practice as well as providing a critical perspective on the capabilities and limitations of modeling at various level of approximation. Topics will include will be molecular visualization (VMD, Pymol), QM methods for electronic structure (Gaussian), all-atom and coarse-grained force field development, normal mode analysis (ProDy), Monte Carlo and Molecular Dynamics simulations (AMBER), kinetic master equation simulations for the phenomenological modeling of rate processes. MMS will be accessible at various levels of theoretical and computational rigor, and individualized to the needs and interests of UG and GR students. Prerequisite: Introductory Chemistry.
Texts: Andrew Leach, Molecular Modeling: Principles and Applications, Pearson Prentice Hall, Inc. (free download available). Articles from the original and current scientific literature.