Molecular biophysics iii biomolecular interactions and dynamics
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Molecular Biophysics III: Biomolecular Interactions and Dynamics. Course Directors: Judith Klein-Seetharaman [email protected] Sanford Leuba [email protected] Course TA: Oznur Tastan [email protected] Contact details in the handout. What do we want you to learn in this class?.

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Molecular Biophysics III: Biomolecular Interactions and Dynamics

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Molecular biophysics iii biomolecular interactions and dynamics

Molecular Biophysics III: Biomolecular Interactions and Dynamics

Course Directors:

Judith Klein-Seetharaman [email protected]

Sanford Leuba [email protected]

Course TA:

Oznur Tastan [email protected]

Contact details in the handout.


What do we want you to learn in this class

What do we want you to learn in this class?

  • A. Scholarly goals

  • B. Scientific skills goals

  • C. Presentation goals

  • D. Networking goals


What do we want you to learn in this class and how will we help you reach these goals

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


What do we want you to learn in this class a scholarly goals

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

Data

acq / analysis

Demos

Data analysis

homeworks


What do we want you to learn in this class b scientific skills goals

What do we want you to learn in this class? B. Scientific skills goals

Lectures by you:

lots of papers

  • 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:

key papers

Not all key

papers given

Lectures

by you

Methods

summary

Audience of

lectures by you


What do we want you to learn in this class c presentation goals

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

Lectures

by you

Seminar Series

Methods

summary


What do we want you to learn in this class d networking goals

What do we want you to learn in this class? D. Networking goals

Lectures

by you

  • 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

Seminar Series


Course materials

Course materials

  • Supporting website: 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/

    • Login using your Pitt id (or id provided to you by Oznur)

    • Check on your grades


Lectures prepared by you

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 2nd draft to either Sanford or Judith, go through iterations with them as needed

  • Show xth draft to the expert (student mentor)


Participation

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


Grading scheme

Grading scheme

30%

  • 3 exams

    • 1st exam

    • 2nd 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

10%

10%

10%

20%

5%

20%

25%


Expectations

Expectations

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

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


Mock exam

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


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