Spring 2013

EECS 395/495: Algorithmic DNA Self-Assembly

3:30-4:45 Tuesday and Thursday

Technological Institute Room LG72


Department of Electrical Engineering and Computer Science
Northwestern University


Class URL: www.cs.northwestern.edu/~kao/eecs395-algorithmic-dna-self-assembly


(Last updated 5/1/2013)


**Important Announcements. Please Check Often.**

1. If you are already scheduled for your presentation, please double check your topic title and date. If you are not yet scheduled, please let me know your topic and preferred date very soon. -- 4/26/2013.

Format: seminars open to both graduate and undergraduate students.


Synopsis: Self-assembly is a process by which simple objects autonomously assemble into complex objects. 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 single-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.



Ming-Yang Kao
Office: Tech M324
Phone: 847-230-9867
Email: kao@northwestern.edu
Office Hours: 1:00--2:00 Wednesday and Friday, or by appointment


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 positions funded by National Science Foundation for undergraduate students in the summer.


Meeting Schedule: This schedule is tentative. Details will be added to it as they become available.


o   Week 1: (4/2, 4/4)

o   Tuesday 4/2 -- no class per the class schedule posted by the Registrar.

o   Thursday 4/4 -- syllabus; general introduction.

o   Week 2: (4/9, 4/11)

o   Tuesday 4/9 -- the Abstract Tile Assembly Model; examples, 1 x n rectangle for a give n, 2 x n rectangle for a given n (O(n) tile complexity versus O(sqrt(n)) tile complexity).

o   Thursday 4/11 -- ad hoc versus programming approaches to tile set design; self-assembly for multiple shapes; examples, 1 x n rectangles for all n >= 2, 1 x 3n rectangles for all n, 2 x n rectangles for all n >= 2, n x n squares for all n >= 2.

o   Week 3: (4/16, 4/18)

o   Each student should meet with the Instructor by this week to pick a topic for her/his presentations.

o   Tuesday 4/16 -- n x n squares for all n >= 2.

o   Thursday 4/18 -- 2 x n rectangle for a given n.

o   Week 4: (4/23, 4/25)

o   Tuesday 4/23 -- generalized tile self-assembly models; use 2 temperatures to reduce the tile complexity for the k x n rectangle for given k and n.

o   Thursday 4/25 -- generalized tile self-assembly models; use flexible glues to reduce the tile complexity for the k x n rectangle for given k and n.

o   Week 5: (4/30, 5/2)

o   Presentations by students will start this week.

o   Tuesday 4/30 -- Presenter: Aleck Johnsen. Topic: Tile Self-Assembly for Colored Patterns.

o   Thursday 5/2 -- Presenter: Michael William Tu. Topic: Detection of Pathogens with Self-Assembled DNA Aptamer Arrays and Fluorescence Nanobarcodes.

o   Week 6: (5/7, 5/9)

o   Tuesday 5/7-- Presenter: Erlin Zylalaj. Topic: Software Package www.nupack.org.

o   Thursday 5/9 -- Presenter: Xiangyi Xie. Topic: Turing Universality of Step-Wise and Stage Assembly at Temperature 1 (Bahar Behsaz, Jan Manuch, and Ladislav Stacho).

o   Week 7: (5/14, 5/16)

o   Tuesday 5/14 -- Presenter: Brian Michael Ambielli. Topic: Survey of the Applications of Three Dimensional Self Assembly.

o   Thursday 5/16 -- Presenter: George James Wheaton. Topic: Programmable Self-Assembly (Eric Klavins).

o   Week 8: (5/21, 5/23)

o   Tuesday 5/21: Presenter: Suhan Ma. Topic: Simple Evolution of Complex Crystal Species (Rebecca Schulman,

Erik Winfree).

o   Thursday 5/23: Presenter: Christina Burghard. Topic: Three-Dimensional Structures Self-Assembled from DNA Bricks (Yonggang Ke et al.). (35 minutes)

o   Thursday 5/23: Presenter: Donghan Miao. Topic: An Improved DNA-Sticker Addition Algorithm and Its Application to Logarithmic Arithmetic (Mark G. Arnold). (35 minutes)

o   Week 9: (5/28, 5/30)

o   Tuesday 5/28 -- Presenter: Fangzhou Sun. Topic: One-Dimensional Staged Self-Assembly.

o   Thursday 5/30 -- Presenter: Sudarshan Srivatsan. Topic: DNA Walkers.

o   Week 10: (6/4, 6/6)

o   Tuesday 6/4: Presenter: Nan Wu. Topic: DNA Origami (Paul W. K. Rothemund).

o   Thursday 6/6: Presenter: Irsal Jasebel Alsanea. Topic: Cellular Automata Self-assembly Modeling.

o   Week 11: (6/11, 6/13)

o   No class.

o   The survey paper is due via email to the Instructor by midnight Thursday 6/13/2013.


List of Topics and Papers: This list is tentative and will be updated based on the interests of the participants of this course.


A.  Basic Models -- The Abstract Tile Assembly Model (definitions and examples, 2 meetings)

B.  Tile Complexity (square, upper and lower bounds, optimal bound, 4 meetings)

C.  Universal Computation (simulations, 2 meetings)

D. Generalized Models (2 meetings)

E.  Temperature Programming (2 meetings)

F.  Concentration Programming (2 meetings)


G. Basic Models -- The Kinetic Tile Assembly Model (definitions)

H. Assembly Time (squares, 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.

1.  Niles Pierce's Lab

2.  John Reif's Lab

3.  Paul W.K. Rothemund's Lab

4.  Erik Winfree's Lab