**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.

** **

**Instructor: **

Ming-Yang
Kao

Office: Tech M324

Phone: 847-230-9867

Email: kao@northwestern.edu

URL: www.cs.northwestern.edu/~kao

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)

[Becker.2006.SAC]

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.