2013-2014 Course Selection Book - SUNY Upstate Medical University

SB 3BIOLOGICAL AND MEDICAL PHYSICS(SU: PHY 615)B6113 Credit HoursCoordinator(s):Instructor(s):Prerequisite(s):Period offered:Dr. Stewart LohLiviu Movileanu;Office: 211 (SU Physics Bldg.)E-mail: lmovilea@physics.syr.edu;Phone: (315) 443-8078SB 3 student orapproval of course coordinator.Fall semesterCourse description: Biological and Medical Physics(PHY 615, 3 credits) is a one-semester graduate levelcourse intended for students from physical, chemicalandbiomedical sciences. The PhD students enrolledin Structural Biology, Biochemistry and BiophysicsProgram (SB 3 ), or those from Biotechnology and BiomedicalSciences Programs (SUNY-ESF, SU and UpstateMedical School) are very welcome. From the verybeginning, I have to mention that this is not a courseto teach either “biology for physicists” or “physics forbiologists and physicians”. The emphasis will be on aselected range of “hot topics” that lie at the interfacebetween physical, chemical and biomedical sciences.The primary aim is to have an overview of the fundamentalbiophysical research questions, as well asrecent experimental developments and techniquesthat engage a multidisciplinary effort. In addition, wewill discuss “applicative topics” of biological physics inseveral realms, including nanobiotechnology, biosensors,drug delivery, and medical imaging. Therefore,much of the content of PHY 615 will not be presentedin a traditional manner. Finally, from a practical pointof view, the Biological and Medical Physics course willestablish strategies for people with complementarybackgrounds who will be having the chance to workin multidisciplinary areas.MOLECULAR MODELING (SU: BCM684)B6543 Credit HoursCoordinator(s):Instructor(s):Prerequisite(s):Period Offered:Dr. Stewart LohDr. Tom Duncan (UMU),Dr. Phil Borer (SU),SB 3 student orapproval of course coordinator.Spring semester of odd yearsCourse Description: Enrollment: Limited to 15students. Students will become proficient inmolecular modeling by attending lectures andcompleting projects using available work stations.Topics covered include the following:1. Unix survival skills2. Download and modify protein data bank files3. Visualization and rendering4. Strategies for minimization and dynamics5. Energy and simulation temperature6. Kinetic analysis of a two-state jump7. Dynamics of an inhibitor bound to HIV- Iprotease8. Simulating statistical behavior of the alphahelix-coil transition9. Introduction to protein homology modeling10. Protein sequence analysis and alignment11. Classification and recognition of protein foldingmotifs12. Approaches to three-dimensional modeling ofproteins13. Evaluation and refinement of three-dimensionalmodels17