This course covers theoretical models of molecular computing, DNA computing, and algorithmic self-assembly, with an emphasis on algorithmic design and analysis of self-assembling systems. Mathematical and algorithmic topics are covered along with the experimental motivation behind the models. The course will focus on models of unconventional and natural computation stemming from a selection of recently published research papers. Specific topics will includes DNA self-assembly, algorithmic tile self-assembly, DNA codeword design, and chemical reaction networks.
· LaTex LaTex is the standard document preparation software used to write scientific papers.
o Sample latex file with figures and bibliography
§ Should produce this pdf
· WinEdt A widely used text editor with plugins for LaTex.
· Inkscape A widely used vector graphics program for making figures.
· VersaTILE self-assembly simulator
- aTAM introduction, rectangle building: Slides
- Homework: rectangleHomework (due 1/29)
- aTAM square building: Slides
- aTAM optimal square building
o Unique glue pairing model: notes
o Flexible glues model: slides
· Week 6: Read: The Tile Complexity of Linear Assemblies
1. Additional reading: Concentration independent random number generation in tile self-assembly
· Week 7: Open Problems. Homework: openProblems (due 3/21)
1. aTAM Assembly Verification Problems, Read: Combinatorial Optimization Problems in Self-Assembly
2. Pattern Assembly Problems, Read: Binary Pattern Tile Set Synthesis Is NP-Hard
3. Feature Assembly Problems, Read: Just think and discuss to come up with creative ideas
· Week 9: Verification problems, open problems 2ham-UAV
· Week 10: Discrete counts: homework (due 4/2)
· Week 11: Final project: finalProject