ECS 289A: Theory of Molecular Computation
Winter 2021
Instructor
Dave Doty
doty@ucdavis.edu
Office: Zoom link
Office hours: Wed 10:0011:00am
Lectures
Tuesday and Thursday, 9:0010:20am, Zoom link
Course objective
To study the fundamental abilities and limits to the engineering of automated (i.e., computational) molecular systems, in a mathematically rigorous way.
Prerequisites
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 12 of Probability in Computing: Randomized Algorithms and Probabilistic Analysis, by Mitzenmacher and Upfal.
Campuswire
The Campuswire page
for the course can be used to ask questions about the course and
homework.
Please use Campuswire instead of email unless the question is of a personal nature.
Notes
lecture notes (note that these are not
comprehensive since I often take material straight from a paper)
Slides
slides (these are new this quarter, not as detailed as the notes, but I hope to be a bit easier to follow)
Homework
There is a Canvas page with the homework posted.
Project
Project ideas
Schedule
Algorithmic tile selfassembly

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 ProgramSize Complexity of SelfAssembled Squares,
O(log n / log log n) tile types sufficient to assemble an n x n square
paper: Running Time and Program Size for Selfassembled Squares

Tues, Jan 12, 2021
formal definition of the aTAM

Thurs, Jan 14, 2021
simulation of Turing machine with a tile assembly system
assembling scaledup version of any finite shape from optimal number of tile types
paper:
Complexity of SelfAssembled Shapes,
computable shape not strictly selfassembled by any TAS
paper:
Strict SelfAssembly of Discrete Sierpinski Triangles,
computable set not weakly selfassembled by any TAS
paper:
Computability and Complexity in SelfAssembly

Tues, Jan 19, 2021
concentration programming
paper: Randomized selfassembly for exact shapes
finite shape that requires more tile types to strictly selfassemble with a directed TAS than a nondirected TAS
paper: The Power of Nondeterminism in SelfAssembly