Instructor: Ashish Goel (Office Hours: Tue 1-2)
Essential Class Information: Syllabus, Grading policy, Timetable etc.
Announcements: HW 1 is now online. Also, there is no class on Thu, Apr 22nd. Please use this time to do the background work mentioned in HW1.
Description: Self-assembly is the ubiquitous process by which objects autonomously assemble into complexes. Nature provides many examples: Atoms react to form molecules. Molecules react to form crystals and supramolecules. Cells coalesce to form organisms. Precisely controlled molecular self-assembly has the potential to be a whole new engineering paradigm, much like the engine and the semiconductor. It will enable nano-machines, computation at the molecular level, fractal antennas, and molecular circuits, among other things.
DNA is a natural candidate for molecular self-assembly. It has the right size, its functionality is determined largely by its combinatorics rather than geometry, and nature offers a "proof of concept" for DNA self-assembly.
In this class, we will develop models and algorithms to facilitate efficient and robust self-assembly at the nano scale. We will study self-assembly from combinatorial, optimization, and stochastic viewpoints. We will point out the broad topics where further mathematical research is urgently needed. We will also describe some of the recent experimental advances in DNA self-assembly, and the applications which motivate these experiments.
Grading: There will be four homework assignments, one of which will be an open-ended research project and another will be a take-home midterm. It is expected that most of the students will register for this class using the P/NC option. For these students, there will be no final exam – your grade will be determined by class participation and your performance on the homework assignments. If you are signed up for a letter grade, please let me know in advance – you will be given an extra take home exam.
Collaboration Policy: No collaboration is allowed on any of the homework assignments unless explicitly permitted.
What is molecular self-assembly?
An abstract combinatorial model for DNA self-assembly
Universal computation using self-assembly
Assembly time and design complexity of self-assembled systems
Constructing counters using self-assembly – the difference between natural and engineered self-assembly
3/31/04. Note to auditors: Please subscribe to the email list msande319-spr0304-guests using https://lists.stanford.edu
4/20/04. HW 1 is now online. Due 4/30.
4/20/04. There will be no class on Thu, 4/22. Please use this time to do the background work mentioned in HW1.