
Fall 2018 ENGR 1.236
This
course covers theoretical models of molecular computing, DNA computing, and
algorithmic selfassembly, with an emphasis on algorithmic design and
analysis of selfassembling 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 selfassembly, algorithmic tile selfassembly, DNA codeword
design, and chemical reaction networks. class syllabus
Robert
Schweller
·
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 selfassembly simulator

aTAM introduction, rectangle building: Slides 
Homework: rectangleHomework
(due 1/29)

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 selfassembly ·
Week 7: Open Problems. Homework: openProblems (due 3/21) 1.
aTAM Assembly Verification Problems, Read: Combinatorial Optimization Problems in
SelfAssembly 2.
Pattern Assembly Problems,
Read: Binary
Pattern Tile Set Synthesis Is NPHard 3.
Feature Assembly Problems,
Read: Just think and discuss to come up with creative ideas ·
Week 9: Verification problems,
open problems 2hamUAV 1.
2hamUAV hardness: 2D,
high temperature, 3D constant temperature ·
Week 10: Discrete counts: homework
(due 4/2) ·
Week 11: Final project: finalProject

