Fall 2018
Molecular Computation
MW 3:05pm – 4:20pm

ENGR 1.236
Department of Computer Science
University of Texas - Rio Grande Valley


This course covers theoretical models of molecular computing, DNA computing, and algorithmic self-assembly, with an emphasis on algorithmic design and analysis of self-assembling systems. Mathematical and algorithmic topics are covered along with the experimental motivation behind the models. The course will focus on models of unconventional and natural computation stemming from a selection of recently published research papers.  Specific topics will includes DNA self-assembly, algorithmic tile self-assembly, DNA codeword design, and chemical reaction networks.

class syllabus




Robert Schweller
Office: ENGR 3.294
Phone: (office) 956-665-2667  (cell) 773-456-1722
Email: schwellerr@gmail.com
URL: http://faculty.utrgv.edu/robert.schweller/
Office Hours: Tue, Thur 11:00-12:00, Wed 10:00-12, or by appointment



Software to install:

·         LaTex LaTex is the standard document preparation software used to write scientific papers.

o   Sample latex file with figures and bibliography

§  Source

§  Should produce this pdf

·         WinEdt A widely used text editor with plugins for LaTex.

·         Inkscape A widely used vector graphics program for making figures.

·         VersaTILE self-assembly simulator


Weekly Reading Assignments and Projects:

-          aTAM introduction, rectangle building: Slides

-          Homework: rectangleHomework (due 1/29)

  • Week 2: quiz:  Provide a 10 tile-type aTAM system that uniquely assembles a 6 x 6 square.

-          aTAM square building: Slides

-          aTAM optimal square building

o   Unique glue pairing model: notes

o   Flexible glues model: slides

·         Week 6: Read: The Tile Complexity of Linear Assemblies

1.       Additional reading: Concentration independent random number generation in tile self-assembly  

·         Week 7: Open Problems. Homework: openProblems (due 3/21)

1.      aTAM Assembly Verification Problems, Read: Combinatorial Optimization Problems in Self-Assembly

2.      Pattern Assembly Problems, Read: Binary Pattern Tile Set Synthesis Is NP-Hard

3.      Feature Assembly Problems, Read: Just think and discuss to come up with creative ideas

·         Week 9: Verification problems, open problems 2ham-UAV

1.      2ham-UAV hardness: 2D, high temperature, 3D constant temperature

·         Week 10: Discrete counts:  homework (due 4/2)

·         Week 11: Final project: finalProject