ECS 289A: Theory of Molecular Computation
Winter 2018

Course announcement (PDF)

Instructor

Dave Doty
doty@ucdavis.edu
Office: 2069 Academic Surge
Office hours: Tues 2:10-3:00pm

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 1-2 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, 12:10-1:30pm, Olson 144

Algorithmic tile self-assembly

  1. 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)
  2. 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
  3. Tues, Jan 16, 2018
    formal definition of the aTAM
  4. Thurs, Jan 18, 2018
    Brief introduction to Kolmogorov complexity
    Ω(log n / log log n) tile types necessary to assemble an n x n square
    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
  5. Tues, Jan 23, 2018
    simulation of Turing machine with a tile assembly system
    assembling scaled-up version of any finite shape from optimal number of tile types
    paper: Complexity of Self-Assembled Shapes
  6. Thurs, Jan 25, 2018

Chemical reaction networks

  1. Tues, Jan 30, 2018
    Introduction to chemical reaction networks (CRNs). Examples of stable function computation.
    paper (functions): Deterministic Function Computation with Chemical Reaction Networks
  2. Thurs, Feb 1, 2018
    Formal definition of stable function computation.
    Examples of stable predicate computation.
    Formal definition of stable predicate computation.
    paper (predicates): Computation in Networks of Passively Mobile Finite-State Sensors
  3. Tues, Feb 6, 2018
    Definition of semilinear sets and functions, claim that only they can be stably computed.
    Formal definition discrete chemical kinetic model (Gillespie model).
    Derivation of expected completion times for some simple CRNs.
    paper: Exact stochastic simulation of coupled chemical reactions
  4. Thurs, Feb 8, 2018
    time complexity analysis of computing functions/predicates with CRNs
    Register machines.
    Simulation of register machines by CRNs with a large probability of error.
    paper:
  5. Tues, Feb 13, 2018
    Turing-universality: simulation of register machines by CRNs with a small probability of error.
    paper: Computation with Finite Stochastic Chemical Reaction Networks
    paper: Fast Computation by Population Protocols With a Leader
  6. Thurs, Feb 15, 2018
    Every semilinear set can be stably decided by a CRN.
    paper: Computation in Networks of Passively Mobile Finite-State Sensors
  7. Tues, Feb 20, 2018
    Only semilinear sets can be stably decided by a CRN.
    paper: Stably Computable Predicates are Semilinear

DNA strand displacement

  1. Thurs, Feb 22, 2018
    Introduction to DNA strand displacement.
    Visual DSD (simulation tool)
    papers:

Thermodynamic binding networks

  1. Tues, Feb 27, 2018
    Thermodynamic binding networks
    Boolean circuits
    paper: Thermodynamic binding networks
    slides
  2. Thurs, Mar 1, 2018
    Thermodynamic binding networks
    Exponential size bound on stable polymers
    aTAM counter that is thermodynamically stable

Experimental self-assembly

  1. Tues, Mar 6, 2018
    Introduction to DNA origami.
    Design of geometric molecular bonds
    papers:
    Programmable molecular recognition based on the geometry of DNA nanostructures
    Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components
    Design of geometric molecular bonds
  2. Thurs, Mar 8, 2018
    Algorithmic self-assembly with single-stranded tiles.

Project presentations

  1. Tues, Mar 13, 2018
    Project presentations
  2. Thurs, Mar 15, 2018
    Project presentations