- Announcing an NSM special topics course for Spring 2001-

Molecular Dynamics and Molecular Modeling

Produced by the Beveridge Lab Group -- Directed by Dr. Yongxing Liu

                   Chem 388:   Meets Tue/Thur    9:00 – 10:30 AM    SCI 074

This course is designed to introduce graduate students and advanced undergraduate science majors to the subject of computer simulation of molecules and macromolecules in fluids, liquids and solutions. This course is a basic introduction to the fundaments of molecular dynamics (MD) and also Monte Carlo (MC) computer simulation, and how these techniques are applied in molecular physics, structural biology and  pharmaceutical design.  Part I of the course will treat the fundamentals of molecular dynamics simulation illustrated by applications to simple fluids of  hard spheres and soft spheres. In part II, applications to molecular liquids will be considered,  illustrated by computer simulations of  the structure and thermodynamic properties of liquid water.  Part III introduces all atom  MD simulations on proteins, DNA, and  RNA molecules in solution, with  consideration of  related methods  based on continuum electrostatics. Part IV will be presentations on topics of current interest in molecular modeling, such as protein folding and structure prediction, DNA bending, ligand binding, and pharmaceutical design. A series of computer-based homework exercises will be provided in order that participants in the class can gain a hands-on familiarity and experience with molecular simulation and computer graphics analysis of the results.