ECS 289A: Theory of Molecular Computation
Office: 2069 Academic Surge
Office hours: Tues 2:10-3:00pm
To study the fundamental abilities and limits to the engineering of automated (i.e., computational) molecular systems, in a mathematically rigorous way.
ECS 120 or equivalent (familiarity with Chapters 1,3,4,7 of Introduction to the Theory of Computation by Sipser).
Prior experience with probability theory is useful; in particular, Chapters 1-2 of Probability in Computing: Randomized Algorithms and Probabilistic Analysis, by Mitzenmacher and Upfal.
The Piazza page
for the course can be used to ask questions about the course and
Use access code "ecs289a" to enroll.
Please read this warning about Piazza as well.
lecture notes (note that these are not
comprehensive since I often take material straight from a paper)
There is a Canvas page with the homework posted.
Tuesday and Thursday, 12:10-1:30pm, Olson 144
Algorithmic tile self-assembly
Tues, Jan 9, 2018
Introduction to abstract Tile Assembly Model (aTAM)
aTAM video introduction
ISU TAS simulator
pyTAS (newer version, easier to install, fewer features, likely to have more bugs)
Thurs, Jan 11, 2018
tile complexity of assembling squares
O(log n) tile types for assembling an n x n square
paper: The Program-Size Complexity of Self-Assembled Squares
Tues, Jan 16, 2018
formal definition of the aTAM
Thurs, Jan 18, 2018
Brief introduction to Kolmogorov complexity
Ω(log n / log log n) tile types required to assemble an n x n square
O(log n / log log n) tile types suffice to assemble an n x n square
paper: Running Time and Program Size for Self-assembled Squares
Tues, Jan 23, 2018
assembling scaled-up version of any finite shape from optimal number of tile types
paper: Complexity of Self-Assembled Shapes