This writing intensive course, intended for advanced undergraduate and beginning graduate students in physical and life sciences, provides a practical introduction to the study of the structure and function of biomolecular systems (e.g., proteins) by employing computational methods and theoretical concepts familiar from the physical sciences. In particular, the aims of the course are to: (1) introduce the main computer simulations techniques (e.g., molecular dynamics, Monte Carlo, quantum chemistry) used in modern computational biology; (2) familiarize the students with the use of computer simulation and molecular visualization software; (3) present the basics of both equilibrium and non-equilibrium statistical mechanics methods for analyzing the simulation data; and (4) apply the learned simulation and analysis methods to a variety of case studies of current research interest (e.g., ion and molecular transport through channel proteins and carbon nanotubes, force generation by mechanical  proteins, electronic excitations in photosynthetic protein complexes). The course will have a strong “hands on” character through the in-class and online computer demos and tutorials, regular writing intensive homework assignments and comprehensive term project.

Grading will be based on: (1) homework assignments (handed in electronically as a brief report); (2) a research term project (equivalent to a final exam) due at the end of the semester in electronic form as a research paper, and delivered in front of the class as a 10 min oral presentation during the last week of class; and (3) attendance and participation in the class.  The total number of points assigned to each of these components are as follows:

Provided that you hand in all your homework and final term project and do not miss more than two classes, you may expect the following course grade:
   

For     0-499 points:	F
For 500-649 points:	D
For 650-749 points:	C
For 750-849 points:	B
For 850-1000 points:	A

You fail the class automatically if you miss more than 2 classes, or 1 homework, or the final term project !

Students who have special conditions as addressed by the Americans with Disabilities Act (ADA), and who need any test or course materials to be furnished in an alternative format, should notify the instructor immediately. Reasonable efforts will be made to accommodate the needs of these students. Such students should also register with the Disability Services, A038 Brady Commons, phone 882-4696.