1. Molecular Biophysics III: Biomolecular Interactions and Dynamics Course Directors: Judith Klein-Seetharaman jks33@pitt.edujks33@pitt.edu Sanford Leuba leuba@pitt.eduleuba@pitt.edu Course TA: Oznur Tastan oznur@cs.cmu.eduoznur@cs.cmu.edu Contact details in the handout.

2. What do we want you to learn in this class? A. Scholarly goals B. Scientific skills goals C. Presentation goals D. Networking goals

3. What do we want you to learn in this class and how will we help you reach these goals? Lectures and review sessions by course directors Lectures prepared and given by you Summary of method written by you Tutorials on data acquisition and analysis Hands-on wet lab demos Homeworks: analysis of real experimental data Integration with the Seminar Series Lectures by course directors Lectures by you Methods summary Data acq / analysis Demos Data analysis homeworks Seminar Series

4. What do we want you to learn in this class? A. Scholarly goals Goal: Obtain a rough idea of the current state of understanding of some of the major questions in biomolecular interactions and dynamics Goal: Know how knowledge was obtained. Goal: Given any biological question, provide ideas on how to address this question using biophysical approaches Goal: Be able to weigh different biophysical approaches against each other in terms of –Complementary information –Applicability –Limitations Goal: Get a practical idea and hands-on experience of some of the major biophysical techniques Lectures by course directors Lectures by you and the others Demos Data analysis homeworks Data acq / analysis

5. What do we want you to learn in this class? B. Scientific skills goals Goal: Be able to skim through papers to extract most relevant information fast Goal: Be able to read a paper in depth to understand all the details Goal: Be able to identify which papers that are not part of the starting set of papers are important to get and read Goal: Be able to synthesize the most important information from a large pool of information Goal: Be able to ask scientific questions –Identify what it is that you don’t understand –Identify holes in somebody else’s scientific reasoning or presentation –Place information you obtain into context and identify what would be logical next steps in addressing a given problem, or what would be the next open questions that arise from a scientific result Lectures by you: lots of papers Methods summary Lectures by you: key papers Not all key papers given Lectures by you Audience of lectures by you

6. What do we want you to learn in this class? C. Presentation goals Goal: Prepare well-structured, logical and understandable presentations Goal: Be able to ask and answer questions Goal: Be able to write a readable overview summary of a set of scientific publications Lectures by you Methods summary Seminar Series Lectures by you

7. What do we want you to learn in this class? D. Networking goals Goal: Promote interactions between students and faculty Goal: Prepare you to become an active member of the Structural Biology and Molecular Biophysics Seminar Series –Be able to ask questions in the discussion immediately following the seminar –Discuss science with the seminar speakers Lectures by you Seminar Series

8. Course materials Supporting website: http://www.cs.cmu.edu/afs/cs.cmu.edu/project/structure- 9/Courses/MB3/S07/ http://www.cs.cmu.edu/afs/cs.cmu.edu/project/structure- 9/Courses/MB3/S07/ –Use to view and download syllabus, lecture notes etc. –Use to view and download papers Emailing Judith or Sanford: –Communications regarding presentations (all of the intermediate and the final versions) –Your methods summaries Emailing and/or handing out to Oznur: –Your homeworks –Your exams Blackboard website: https://courseweb.pitt.edu/https://courseweb.pitt.edu/ –Login using your Pitt id (or id provided to you by Oznur) –Check on your grades

9. Lectures prepared by you Read the papers Identify additional papers if needed Make first draft of presentation that includes –Overview of the field –Present key findings –Where does the field stand now? –What are open questions? Show first draft to Oznur if you have difficulties with the English Show first or 2 nd draft to either Sanford or Judith, go through iterations with them as needed Show x th draft to the expert (student mentor)

10. Participation Students not presenting still need to read at least the main paper, ideally more You will be judged on your participation, i.e. asking questions

11. Grading scheme 3 exams –1 st exam –2 nd exam –Final exam Lectures prepared and given by you Summary of method overview written by you Participating in asking questions and discussing lectures given by your colleagues Homeworks 30% 10% 20% 5% 20% 25%

12. Expectations From YOU Enthusiasm Attendance and active participation Lectures prepared and given by you are to be seen as projects: we expect you to spend a major amount of time on their preparation Summary of methods overview written by you Feedback: Tell us if you like or don’t like something, preferably immediately From US Enthusiasm We will help you as much as we can with the preparation of these lectures Feedback: We will respond to your feedback We will NOT explain the basics of the different techniques in class, you need to read up on the background yourself

13. Mock exam Will not be graded, this is just to get an idea of background knowledge and for you to get an idea of the types of things we hope you will know as a minimum after the course Try to briefly answer as many as possible If you do not know the answer pls write “don’t know” so that we can tell the difference if you didn’t get time to look at a question