Harvard:Biophysics 242r/2011:Schedule: Difference between revisions

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''Course meetings are on Mondays and Wednesdays in CLSB521 from 100 pm to 230 pm, with immediately following optional project sessions from 230 pm to 330 pm; these optional sessions will commence on Wednesday, February 2.''
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| align="center" style="background:#f0f0f0; width:100px;"|'''Date'''
| align="center" style="background:#f0f0f0; width:100px;"|'''Date'''
| align="center" style="background:#f0f0f0; width:150px;"|'''Presenter(s)'''
| align="center" style="background:#f0f0f0; width:150px;"|'''Presenter(s)'''
| align="center" style="background:#f0f0f0;"|'''Topic'''
| align="center" style="background:#f0f0f0;"|'''Topic'''
| align="center" style="background:#f0f0f0;"|'''Slides'''
|-
|-
| [[Harvard:Biophysics_242r/2011/01|Monday, January 24 (Session 1)]]||William Shih||Course Overview, midterm projects, DNA nano primitives||[[Media:HarvardBiophysics242r2011-session1.pdf|pdf]]
| Monday, January 24 (Session 1)||William Shih||Course Overview, midterm projects, biomolecular nano primitives
|-
|-
| [[Harvard:Biophysics_242r/2011/02|Wednesday, January 26 (Session 2)]]||John Sadowski||DNA visualization (nanoEngineer and (PyMol or CCP4)) software demo ||[[Media:HarvardBiophysics242r2011-session2.pdf|pdf]]
| Wednesday, January 26 (Session 2)||John Sadowski||<div style="color:green">software demo: nanoEngineer for biomolecular visualization</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/03|Monday, January 31 (Session 3)]]||William Shih||Origami and large structures||[[Media:HarvardBiophysics242r2011-session3.pdf|pdf]]
| Monday, January 31 (Session 3)||William Shih||Origami and large structures
|-
|-
| [[Harvard:Biophysics_242r/2011/04|Wednesday, February 2 (Session 4)]]||William Shih||caDNAno software demo||[[Media:HarvardBiophysics242r2011-session4.pdf|pdf]]
| <div style="color:red">CANCELLED</div> Wednesday, February 2||||
|-
|-
| [[Harvard:Biophysics_242r/2011/05|Monday, February 7 (Session 5)]]||Dave Zhang||DNA base-pairing biophysics and informational circuits||[[Media:HarvardBiophysics242r2011-session5.pdf|pdf]]
| Monday, February 7 (Session 4)<br><div style="color:green">Special location: NRB335</div>||Dave Zhang||DNA base-pairing biophysics and informational circuits
|-
|-
| [[Harvard:Biophysics_242r/2011/06|Wednesday, February 9 (Session 6)]]||Adam Marblestone||NuPack sequence design (manual versus automated sequence selection)||[[Media:HarvardBiophysics242r2011-session6.pdf|pdf]]
| Wednesday, February 9 (Session 5)||William Shih||<div style="color:green">software demo: caDNAno for DNA-origami design</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/07|Monday, February 14 (Session 7)]]||Peng Yin||Dynamic DNA nanomachines||[[Media:HarvardBiophysics242r2011-session7.pdf|pdf]]
| Monday, February 14 (Session 6)||Peng Yin||Dynamic DNA nanomachines
|-
|-
| [[Harvard:Biophysics_242r/2011/08|Wednesday, February 16 (Session 8)]]||Adam, John, Peng, William||Software recitation session (questions and more exercises)||[[Media:HarvardBiophysics242r2011-session8.pdf|pdf]]
| Wednesday, February 16 (Session 7)||Adam Marblestone||<div style="color:green">software demo: NuPack for sequence analysis and design</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/09|Monday, February 21 (Session 9)]]||Peng Yin||Current applications in DNA nanotechnology||[[Media:HarvardBiophysics242r2011-session9.pdf|pdf]]
| Monday, February 21||||<div style="color:red">no class meeting (President's Day)</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/10|Wednesday, February 23 (Session 10)]]||Vatsan Raman||Computational Protein Design||[[Media:HarvardBiophysics242r2011-session10.pdf|pdf]]
| Wednesday, February 23 (Session 8)||Vatsan Raman||Computational Protein Design
|-
|-
| [[Harvard:Biophysics_242r/2011/10|Monday, February 28 (Session 11)]]||Vatsan Raman||FoldIt and Rosetta Protein Design||[[Media:HarvardBiophysics242r2011-session11.pdf|pdf]]
| Monday, February 28 (Session 9)||Vatsan Raman||<div style="color:green">software demo: FoldIt and Rosetta Protein Design</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/12|Wednesday, March 2 (Session 12)]]||||Midterm Presentations I||[[Media:HarvardBiophysics242r2011-session12.pdf|pdf]]
| Wednesday, March 2 (Session 10)||students||Midterm Presentations <div style="color:purple">we may start early and end late; stay tuned for updates</div>
|-
|-
| Monday, March 7||||Biophysical Society Meeting (no class meeting)
| Monday, March 7|||| <div style="color:red">no class meeting (Biophysical Society Meeting)</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/13|Wednesday, March 9 (Session 13)]]||||Midterm Presentations II||[[Media:HarvardBiophysics242r2011-session13.pdf|pdf]]
| Wednesday, March 9 |||| <div style="color:red">no class meeting (Biophysical Society Meeting)</div>
|-
|-
| March 15||||Spring Break (no class meeting)||
| Monday, March 14||||<div style="color:red">no class meeting (Spring Break)</div>
|-
|-
| March 17||||Spring Break (no class meeting)||
| Wednesday, March 16||||<div style="color:red">no class meeting (Spring Break)</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/10|Monday, March 21 (Session 14)]]||Adam Marblestone||Methods for nanoscale-device characterization||[[Media:HarvardBiophysics242r2011-session14.pdf|pdf]]
| Monday, March 21 (Session 11)||Peng Yin || Applications of DNA/RNA nanotechnology
|-
|-
| [[Harvard:Biophysics_242r/2011/15|Wednesday, March 23 (Session 15)]]||George Church||Minimal in vitro replicating systems; hybrid electronic-biochemical systems||[[Media:HarvardBiophysics242r2011-session15.pdf|pdf]]
| Wednesday, March 23 (Session 12)||Adam Marblestone/Tom Schaus||Methods for nanoscale-device characterization/<div style="color:green">software demo: Nucleic-acid kinetic simulation</div>
|-
|-
| [[Harvard:Biophysics_242r/2011/16|Monday, March 28 (Session 16)]]||Joanna Aizenberg||Bioinspired Actuation Systems||[[Media:HarvardBiophysics242r2011-session16.pdf|pdf]]
| Monday, March 28 (Session 13)||Joanna Aizenberg||Sea sponges: A textbook in materials physics
|-
|-
| [[Harvard:Biophysics_242r/2011/17|Wednesday, March 30 (Session 17)]]||Milan Stojanovic||Creepy Spiders||[[Media:HarvardBiophysics242r2011-session17.pdf|pdf]]
| Wednesday, March 30 (Session 14)||Milan Stojanovic|| 1. Designs and Evolutions of Chemical Noses
 
2. Molecular Computing based on Nucleic Acid Catalysts
 
|-
|-
| [[Harvard:Biophysics_242r/2011/18|Monday, April 4 (Session 18)]]||Feng Zhang||Engineering DNA-binding proteins: zinc fingers versus Tal||[[Media:HarvardBiophysics242r2011-session18.pdf|pdf]]
| Monday, April 4 (Session 15)||Feng Zhang||Engineering DNA-binding proteins: zinc fingers versus Tal
|-
|-
| [[Harvard:Biophysics_242r/2011/19|Wednesday, April 6 (Session 19)]]||Shawn Douglas||next generation caDNAno software demo||[[Media:HarvardBiophysics242r2011-session19.pdf|pdf]]
| Wednesday, April 6 (Session 16)||Shawn Douglas||<div style="color:green">software demo: caDNAno v2 for DNA-origami design </div>
|-
|-
| [[Harvard:Biophysics_242r/2011/20|Monday, April 11 (Session 20)]]||Instructor||session title (WS away at FNANO)||[[Media:HarvardBiophysics242r2011-session20.pdf|pdf]]
| Monday, April 11 (Session 17) ||Neel Joshi||Peptide and protein self-assembly with a focus on rational design of new assembly modes (Note: core staff away at FNANO Meeting)
|-
|-
| [[Harvard:Biophysics_242r/2011/21|Wednesday, April 13 (Session 21)]]||Neel Joshi||Peptide and protein design (WS away at FNANO)||[[Media:HarvardBiophysics242r2011-session21.pdf|pdf]]
| Wednesday, April 13 (Session 18)||George Church||Hybrid electronic-biochemical systems
|-
|-
| [[Harvard:Biophysics_242r/2011/22|Monday, April 18 (Session 22)]]||L. Mahadevan||Multistable macromolecular assemblies||[[Media:HarvardBiophysics242r2011-session22.pdf|pdf]]
| Monday, April 18 (Session 19)||L. Mahadevan||Multistable macromolecular assemblies
|-
|-
| [[Harvard:Biophysics_242r/2011/23|Wednesday, April 20 (Session 23)]]||Instructor||session title||[[Media:HarvardBiophysics242r2011-session23.pdf|pdf]]
| Wednesday, April 20 (Session 20)||George Church||Minimal in vitro replicating systems
|-
|-
| [[Harvard:Biophysics_242r/2011/24|Monday, April 25 (Session 24)]]||(potential swap slot for J. Aizenberg)||session title||[[Media:HarvardBiophysics242r2011-session24.pdf|pdf]]
| Monday, April 25 (Session 21)||William Shih||Directed molecular evolution
|-
|-
| [[Harvard:Biophysics_242r/2011/25|Wednesday, April 27 (Session 25)]]||William Shih (potential swap slot for J. Aizenberg)||Directed molecular evolution||[[Media:HarvardBiophysics242r2011-session25.pdf|pdf]]
| Wednesday, April 27 (Session 22)||Peng Yin||Outlook: opportunities and challenges
|-
|-
| [[Harvard:Biophysics_242r/2011/26|Monday, May 2 (Session 26)]]||||Final Presentations I||[[Media:HarvardBiophysics242r2011-session26.pdf|pdf]]
| Monday, May 2 (Session 23)||students||Final Presentations
|-
| [[Harvard:Biophysics_242r/2011/27|Wednesday, May 4 (Session 27)]]||||Final Presentations II||[[Media:HarvardBiophysics242r2011-session27.pdf|pdf]]
|-
|-
|}
|}
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Latest revision as of 07:27, 30 March 2011

Biophysics 242r/2011

Biologically Inspired Molecular Engineering

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Course meetings are on Mondays and Wednesdays in CLSB521 from 100 pm to 230 pm, with immediately following optional project sessions from 230 pm to 330 pm; these optional sessions will commence on Wednesday, February 2.

Date Presenter(s) Topic
Monday, January 24 (Session 1) William Shih Course Overview, midterm projects, biomolecular nano primitives
Wednesday, January 26 (Session 2) John Sadowski
software demo: nanoEngineer for biomolecular visualization
Monday, January 31 (Session 3) William Shih Origami and large structures
CANCELLED
Wednesday, February 2
Monday, February 7 (Session 4)
Special location: NRB335
 Dave Zhang DNA base-pairing biophysics and informational circuits
Wednesday, February 9 (Session 5) William Shih
software demo: caDNAno for DNA-origami design
Monday, February 14 (Session 6) Peng Yin Dynamic DNA nanomachines
Wednesday, February 16 (Session 7) Adam Marblestone
software demo: NuPack for sequence analysis and design
Monday, February 21
no class meeting (President's Day)
Wednesday, February 23 (Session 8) Vatsan Raman Computational Protein Design
Monday, February 28 (Session 9) Vatsan Raman
software demo: FoldIt and Rosetta Protein Design
Wednesday, March 2 (Session 10) students Midterm Presentations
we may start early and end late; stay tuned for updates
Monday, March 7
no class meeting (Biophysical Society Meeting)
Wednesday, March 9
no class meeting (Biophysical Society Meeting)
Monday, March 14
no class meeting (Spring Break)
Wednesday, March 16
no class meeting (Spring Break)
Monday, March 21 (Session 11) Peng Yin Applications of DNA/RNA nanotechnology
Wednesday, March 23 (Session 12) Adam Marblestone/Tom Schaus Methods for nanoscale-device characterization/
software demo: Nucleic-acid kinetic simulation
Monday, March 28 (Session 13) Joanna Aizenberg Sea sponges: A textbook in materials physics
Wednesday, March 30 (Session 14) Milan Stojanovic 1. Designs and Evolutions of Chemical Noses

2. Molecular Computing based on Nucleic Acid Catalysts

Monday, April 4 (Session 15) Feng Zhang Engineering DNA-binding proteins: zinc fingers versus Tal
Wednesday, April 6 (Session 16) Shawn Douglas
software demo: caDNAno v2 for DNA-origami design
Monday, April 11 (Session 17) Neel Joshi Peptide and protein self-assembly with a focus on rational design of new assembly modes (Note: core staff away at FNANO Meeting)
Wednesday, April 13 (Session 18) George Church Hybrid electronic-biochemical systems
Monday, April 18 (Session 19) L. Mahadevan Multistable macromolecular assemblies
Wednesday, April 20 (Session 20) George Church Minimal in vitro replicating systems
Monday, April 25 (Session 21) William Shih Directed molecular evolution
Wednesday, April 27 (Session 22) Peng Yin Outlook: opportunities and challenges
Monday, May 2 (Session 23) students Final Presentations
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