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Spring 2011
4:00-5:20 Monday and Wednesday Tech MG28 Department of
Electrical Engineering and Computer Science Class URL: www.cs.northwestern.edu/~kao/eecs510-algorithmic-dna-self-assembly (last updated 4/6/2011)
**Important
Announcements. Please Check Often.** Please note that the times and room have been changed. 4/6/2011. Synopsis: Self-assembly is a process by
which simple objects autonomously assemble into complexes. It is believed
that self-assembly technology will ultimately permit the precise fabrication
of nanostructures. Self-assembly is common in nature but is not yet well
understood from programming and mathematical perspectives. There are many
kinds of self-assembly. This course will focus on DNA self-assembly. For DNA
self-assembly, double and triple crossover DNA molecules have been designed
to act as four-sided building blocks (which are called tiles). Experimental
work has demonstrated the effectiveness of using these building blocks to
assemble crystals and perform computation. Based on such building blocks,
researchers are actively considering the tile self-assembly model. This model
extends the theory of Wang tilling of the plane by adding a natural mechanism
for growth. The model consists of a set of square tiles where the four sides
of a tile are each associated with a glue (which is implemented as a DNA
strand). A special tile in the tile set is designated as the seed.
Self-assembly takes place by starting with the seed and attaching copies of
tiles from the tile set one by one to the growing seed whenever the total
bonding strength of a tile and the seed is no less than a fixed threshold
(which is implemented as the temperature in the tube). Algorithmic
DNA self-assembly is both a form of nanotechnology and a model of
computation. As a computational model, algorithmic DNA self-assembly first
encodes a computer program for a given computational problem into the glues
of DNA tiles. The tiles then bind with each other to execute the program to
produce a DNA nanostructure, which in turn encodes the desired output of the
computational problem. As a nanotechnology, the goal of algorithmic DNA
self-assembly is to design glues to program a set of tiles to assemble into
the desired nanostructure. This
course will survey results in algorithmic DNA self-assembly and discuss
future research directions. Pre-requisites: A curious mind and basic
mathematical maturity are required. Courses in algorithms, theory of
computation, and computational complexity are preferable but not required. Instructor: Ming-Yang
Kao Course Work: One or more presentations,
active participation in class-room discussions, and a survey paper are
required. Research Opportunities: Optional
original research is strongly encouraged. Collaboration with the Instructor
is also strongly encouraged both during and after this course. There may be
one or two REU positions funded by National Science Foundation available for
undergraduate students in the summer.
Schedule:
This
schedule is tentative. Details will be added to it as they become available.
List
of Topics and Papers: This list is tentative and will be updated based on
the interests of the participants of this seminar course. A. Basic Model --
The Combinatorial Tile Assembly Model (definitions and examples, 2 meeting) B. Tile Complexity
(square, upper and lower bounds, optimal, 4 meetings) C. Universal
Computation (simulations, 2 meetings) D. Generalized
Models (2 meetings) E. Temperature Programming
(2 meetings) F. Concentration
Programming (2 meetings) [Becker.2006.SAC] G. Basic Model --
The Kinetic Tile Assembly Model (definitions) H. Assembly Time
(square, optimization, 2 meetings) I. Error Correction
(2 meetings) J. Staged Assembly
(2 meetings) K. Shape Replication
(2 meetings) L. Self-Assembly
Origami (2 meetings) Course Materials: 1. PPT of the
general introduction List
of Useful Websites:
This list will be updated. |