Harvard:Biophysics 242r/2011/Course Development Log
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Minutes
Thursday, 2010 October 21
- Make it as participatory as possible
- Joint student presentations
- Paper discussions
- Design projects
- DNA origami
- Hairpin devices
- Molecular motors
- Bipedal walker
- Thermal ratchet
- Electrophoretic ratchet
- Rotary motors
- DNA computers
- Integration, precursor, recruiting for BioMOD competition
- Schedule for 2011
- Week 1: Jan. 25 (general overview + listing of midterm projects + DNA nano primitives), 27 (3D visualization demo session)
- Week 2: Jan. 31 (William: overview of origami and higher-order structure), Feb. 3 (caDNAno demo session)
- Week 3: Feb. 8 (Dave Zhang: DNA biophysics), Feb. 10 (NuPack demo session)
- Week 4: Feb. 15 (Peng: hairpins and circuits lecture), Feb. 17 (deterministic and stochastic reaction network simulations)
- Week 5: Feb. 22, Feb. 24
- Week 6: Mar. 1, Mar. 3 (midterm presentations)
- Week 7: Mar. 8 (Biophysical Society Meeting), Mar. 10 (midterm presentations)
- Spring Break
- Week 8: Mar. 22 (survey of natural molecular machines), Mar. 29
- Week 9: Apr. 5, Apr. 7
- Week 10: Apr. 12, Apr. 14
- Week 11: Apr. 19, Apr. 21
- Week 12: Apr. 26, Apr. 28 (first day of reading period)
- Week 13: May 3, May 5 (reading period, final presentations)
- Week 14: May 10, May 12 (exam period)
- Use exam period as buffer in case we need a third presentation day
- Protein engineering
- Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
- Neel: peptide or peptide-like structures
- Joanna Aizenberg: inorganic structure design
- Mahadevan on microtubule design
- Michael Brenner on self-assembly
- Drug delivery, nano
- Top-down nanofabrication
- Radhika: distributed systems
- Computer demo sessions
- caDNAno
- NuPack
- Deterministic and stochastic simulations of reaction networks; how can we integrate this with projects?
- Geometric modeling tool (nanoEngineer); computer visualization
- Class size: project for 15 to 20 students (10–12 Harvard Biophysics, plus some students from other programs, undergrads)
- Do we want to have a limit on course size? perhaps 18 to 20 limit
- What size of group?
- Two to three students per group
- If the course size is 12, that implies 4 to 6 groups (mean of 5 groups)
- If the course size is 20, that implies 7 to 10 groups (mean of 8 groups)
- No more than six groups of people: upper limit on group size of two or three people
- Group presentations for 2 to 3 class meetings
- Course activities (25 sessions total)
- Lectures
- Guest lectures
- Paper discussions
- Project presentations
- Project brainstorming, planning
- Computer exercises/demos
- Laboratory demos
- Centered around group projects
- Experimental realization for some groups near the end
- Ask for sequences, diagrams, simulations
- First half of course
- Group midterm project: selected from restricted list
- Group final project: open-ended
- Proposal guidelines
- Provide aims
- Background for motivation (significance, innovation)
- BioMOD teams asked to register by March 31
- List of team members, graduate teaching fellows, faculty advisors
- Goals
- Get people to be excited about projects
- Get people interested to participate in BioMOD
- First day: Monday, 2011 January 24
- Biophysical Society Meeting: Sat. Mar. 5 to Wed. Mar. 9
- Spring Break: Mar. 12 to Mar. 20
- Last day: Wed., 2011 April 27
- Reading period: Thur. April 28 to Thur., May 5
- Exam period: Friday, May 6 to Sat., May 14
- Grades due May 13
- Adam in charge of course wikis
