ECS 289A: Theory of Molecular Computation
Office: Zoom link
Office hours: Wed 10:00-11:00am
Tuesday and Thursday, 9:00-10:20am, Zoom link
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 Campuswire page
for the course can be used to ask questions about the course and
Please use Campuswire instead of email unless the question is of a personal nature.
lecture notes (note that these are not
comprehensive since I often take material straight from a paper)
slides (these are new this quarter, not as detailed as the notes, but I hope to be a bit easier to follow)
There is a Canvas page with the homework posted.
Algorithmic tile self-assembly
Tues, Jan 5, 2021
Introduction to course,
introduction to abstract Tile Assembly Model (aTAM)
aTAM video introduction
ISU TAS simulator
Thurs, Jan 7, 2021
tile complexity of assembling squares
O(log n) tile types for assembling an n x n square
Ω(log n / log log n) tile types necessary to assemble an n x n square
paper: The Program-Size Complexity of Self-Assembled Squares,
O(log n / log log n) tile types sufficient to assemble an n x n square
paper: Running Time and Program Size for Self-assembled Squares
Tues, Jan 12, 2021
formal definition of the aTAM
Thurs, Jan 14, 2021
simulation of Turing machine with a tile assembly system
assembling scaled-up version of any finite shape from optimal number of tile types
Complexity of Self-Assembled Shapes,
computable shape not strictly self-assembled by any TAS
Strict Self-Assembly of Discrete Sierpinski Triangles,
computable set not weakly self-assembled by any TAS
Computability and Complexity in Self-Assembly
Tues, Jan 19, 2021
paper: Randomized self-assembly for exact shapes
finite shape that requires more tile types to strictly self-assemble with a directed TAS than a non-directed TAS
paper: The Power of Nondeterminism in Self-Assembly