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. The aim of the course is to provide participants with the fundamentals of molecular dynamics and Monte Carlo computer simulation and experience with how these techniques are applied in the areas of molecular physics, structural biology and bioinformatics, and pharmaceutical design. Part I of the course will be devoted to the fundamentals of molecular dynamics simulation as applied to systems such as hard spheres and soft spheres. In Part II, applications in the physics of molecular liquids will be considered, illustrated by computer simulations of the structure and thermodynamics properties of liquid water. In Part III, MD simulations on protein, DNA, and RNA molecules in solution will be treated, including a consideration of methods based on continuum electrostatics. Part IV will consist of special 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 exercises will be provided for participants to gain a hands-on familiarity with molecular simulation and computer graphics analysis of the results.
COURSE FORMAT: Lecture/Discussion
Level: UGRD Credit: 1 Gen Ed Area Dept: NONE Grading Mode: Student Option
Prerequisites: CHEM141 OR CHEM143 OR PHYS111 OR PHYS113
Last Updated on MAR-30-2006
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