Harvard:Biophysics 242r/2011/Course Development Log

Thursday, 2010 October 28

• Scheduling constraints
  • Systems Biology seminar series one Thursday per month from 4 pm to 5 pm
  • Systems Biology faculty meetings Thursdays from 1230 pm to 200 pm
  • BCMP Chalk Talks Thursdays from 1230 pm to 130 pm
  • BCMP Faculty Meetings one Tuesday per month from 2 pm to 330 pm
  • Monday, Wednesday has less constraints
  • We coordinate with Michele

Saturday, 2010 October 23

• Proposed demo sessions

1. Thursday, January 27: Structural DNA visualization software -- NanoEngineer -- John Sadowski
2. Thursday, February 3: Origami design software --- CadNano -- Shawn Douglas
3. Thursday, February 10: Thermodynamic analysis and sequenced design software -- Nupack (and maybe other sequence design software from Winfree group) --- Adam Marblestone
4. Thursday, February 17: Kinetic simulation software --- Dave Zhang

Thursday, 2010 October 21

• Make it as participatory as possible
• Joint student presentations
• Paper discussions
• Design projects

1. DNA origami
2. Hairpin devices
3. Molecular motors
4. Bipedal walker
5. Thermal ratchet
6. Electrophoretic ratchet
7. Rotary motors
8. DNA computers

• Integration, precursor, recruiting for BioMOD competition
• Schedule for 2011

1. Week 1: Jan. 25 (general overview + listing of midterm projects + DNA nano primitives), 27 (3D visualization demo session)
2. Week 2: Jan. 31 (William: overview of origami and higher-order structure), Feb. 3 (caDNAno demo session)
3. Week 3: Feb. 8 (Dave Zhang: DNA biophysics), Feb. 10 (NuPack demo session)
4. Week 4: Feb. 15 (Peng: hairpins and circuits lecture), Feb. 17 (deterministic and stochastic reaction network simulations)
5. Week 5: Feb. 22, Feb. 24
6. Week 6: Mar. 1, Mar. 3 (midterm presentations)
7. Week 7: Mar. 8 (Biophysical Society Meeting), Mar. 10 (midterm presentations)
8. Spring Break
9. Week 8: Mar. 22 (survey of natural molecular machines), Mar. 29
10. Week 9: Apr. 5, Apr. 7
11. Week 10: Apr. 12, Apr. 14
12. Week 11: Apr. 19, Apr. 21
13. Week 12: Apr. 26, Apr. 28 (first day of reading period)
14. Week 13: May 3, May 5 (reading period, final presentations)
15. Week 14: May 10, May 12 (exam period)

• Use exam period as buffer in case we need a third presentation day

• Protein engineering

1. Tal: Feng Zhang?, George Church?: DNA-binding proteins (transcription activator like)
2. 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

1. caDNAno
2. NuPack
3. Deterministic and stochastic simulations of reaction networks; how can we integrate this with projects?
4. 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)

1. Lectures
2. Guest lectures
3. Paper discussions
4. Project presentations
5. Project brainstorming, planning
6. Computer exercises/demos
7. Laboratory demos
8. Centered around group projects
9. Experimental realization for some groups near the end
10. 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

1. Get people to be excited about projects
2. 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