CSCE 5013:  Advanced Special Topics – Algorithmic Self-Assembly

Syllabus                                                                                                                     Spring 2013

Meeting times:  Tues & Thurs 2:00 – 3:20

Location:  JBHT 236

Web site:


Instructor:  Dr. Matthew Patitz

Lab:  JBHT 448

Office:  JBHT 517


Web site:

Office hours:  Tues & Thurs 1:00-2:00, Wed 11-12,

                         and by appointment


Catalog Description:  In-depth introduction to the field of algorithmic self-assembly, which is the application of computational theory and algorithm design to the study and design of nanoscale self-assembling systems.  Many such systems exist in nature, and artificial systems are being developed with the promise of eventually realizing the creation of atomically precise materials and objects and computing with nanoscale components.  Various models of self-assembly will be introduced, along with an up-to-date survey of results in this new and quickly evolving field.  Perspectives to be discussed will include abstract mathematical models, experimentally accurate chemical kinetic models involving DNA (and other) molecules, and software modeling and simulation of both types of models.  Students will utilize and expand knowledge in computational theory, software modeling, and/or chemical systems to engage in novel research projects related to the area.

Beyond introducing the topic of algorithmic self-assembly, the main goal of this course is to:  1) teach students how to acquire fundamental knowledge about a new research area, 2) how to analyze published results, 3) how to develop new ideas for novel research projects, and 4) how to perform research projects from beginning to end, terminating in writing a paper of publishable quality.

Prerequisites:  None.

Textbook:  None, but a variety of research papers will be referenced and serve as recommended reading, with the main course outline following the content contained in An Introduction to Tile-Based Self-Assembly and a Survey of Recent Results (


Final course grades will be determined as a weighted average of the following:

In-class participation:      5-10%

Written summaries:         25%

Every 2 weeks, each student is expected to turn in a 2 page written summary of the content from the previous 2 weeks, especially highlighting interesting open problems.

Homework:                        15%

Approximately 2-3 homework assignments will be given in which students are required to design various self-assembling systems and/or write basic proofs of correctness or impossibility.

Paper presentation:         15%

Each student will give a 30-40 minute presentation of a current paper in the area (selected from a list provided by Matt or approved beforehand).  The presentation should be technically detailed and include an in-depth description of the results.

Project:                               35-40%

The largest portion of final grades will be determined by a novel research project which will be based on a topic approved by Matt in advance.  Students are strongly encouraged to develop their own project ideas, but if help is needed Matt will provide a set of suitable problems/projects ranging from tile assembly constructions, proofs of correctness or impossibility, and programming projects dealing with self-assembly simulators or related software.  This will be due at or near the end of the semester and must include a formal and well-written paper which clearly describes the problem and results.



Academic Integrity:  It is NOT acceptable for a student to use any portion of another student’s work.  Students may discuss problems and solutions with each other, but must implement all submitted work individually.  Suspicious submissions will be forwarded to the All-University Academic Integrity Board.

From the University of Arkansas Provost and Vice Chancellor for Academic Affairs:

As a core part of its mission, the University of Arkansas provides students with the opportunity to further their educational goals through programs of study and research in an environment that promotes freedom of inquiry and academic responsibility. Accomplishing this mission is only possible when intellectual honesty and individual integrity prevail.

Each University of Arkansas student is required to be familiar with and abide by the University’s ‘Academic Integrity Policy’ which may be found at Students with questions about how these policies apply to a particular course or assignment should immediately contact their instructor.

ADA Statement:   If any member of the class has a documented disability and needs special accommodations, the instructor will work with the student to provide reasonable accommodation to ensure the student a fair opportunity to perform in this class. Please advise the instructor of the disability and the desired accommodations and provide the necessary paperwork within the first week of the semester.

Inclement Weather:  If the university is officially closed, class will not be held. In the case of inclement weather, due dates may be postponed, and all such postponements will be posted on the course web site.

Emergency Procedures:  Many types of emergencies can occur on campus; instructions for specific emergencies such as severe weather, active shooter, or fire can be found at  

Severe Weather (Tornado Warning):


Violence / Active Shooter (CADD):