Course Schedule and Catalog

Department: Bioengineering

Grade Mode: Standard Letter

Course Type: Lecture

Credit Hours: 3

Description: COMPUTATIONAL MOLECULAR BIOENGINEERING ***** This is a course designed for students in computationally-oriented biomedical and bioengineering majors to introduce the principles and methods used for the simulations and modeling of macromolecules of biological interest. Protein conformation and dynamics are emphasized. Empirical energy function and molecular dynamics calculations, as well as other approaches, are described. Specific biological problems are discussed to illustrate the methodology. Classic examples such as the cooperative mechanism of hemoglobin and more frontier topics such as the motional properties of molecular motors and ion channels as well as results derived from the current literature are covered. Other potential topics are protein folding/predictions, the nature of reaction rate enhancement in enzyme catalysis, physical chemistry properties of biologically relevant nano-materials, simulations of free energy changes in mutations, electrostatic properties of protein, molecular recognition, and the properties of binding sites. Particular emphasis is also given to the applications of molecular graphics. During the final reading period, each student carries out an original research project that makes use of the techniques and grading is based on the written and oral presentations of the results from the final projects. Suggested prerequisites: college-level calculus, undergraduate level physical chemistry and biochemistry, entry-level thermodynamics and statistical mechanics. ***** Also offered as BIOS 589.