ECS 289A: Theory of Molecular Computation
Winter 2018
Instructor
Dave Doty
doty@ucdavis.edu
Office: 2069 Academic Surge
Office hours: Tues 2:103:00pm
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.
Piazza
The Piazza page
for the course can be used to ask questions about the course and
homework.
Use access code "ecs289a" to enroll.
Please read this warning about Piazza as well.
Notes
lecture notes (note that these are not
comprehensive since I often take material straight from a paper)
Homework
There is a Canvas page with the homework posted.
Project
Project ideas
Lectures
Tuesday and Thursday, 12:101:30pm, Olson 144
Algorithmic tile selfassembly

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 ProgramSize Complexity of SelfAssembled 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 Selfassembled Squares

Tues, Jan 23, 2018
assembling scaledup version of any finite shape from optimal number of tile types
paper: Complexity of SelfAssembled Shapes