BE/CS/CNS/Bi 191ab:  Biomolecular Computation
Professor: Erik Winfree
TA: Niranjan Srinivas

This page is for Winter/Spring 2011. The page for Fall 2011 is different.
Description from the course catalog:
BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) second term; (2-4-3) third term. Prerequisite: ChE/BE 163. Recommended: CS 21, CS 129 ab, or equivalent. This course investigates computation by molecular systems, emphasizing models of computation based on the underlying physics, chemistry, and organization of biological cells. We will explore programmability, complexity, simulation of and reasoning about abstract models of chemical reaction networks, molecular folding, molecular self-assembly, and molecular motors, with an emphasis on universal architectures for computation, control, and construction within molecular systems. If time permits, we will also discuss biological example systems such as signal transduction, genetic regulatory networks, and the cytoskeleton; physical limits of computation, reversibility, reliability, and the role of noise, DNA-based computers and DNA nanotechnology. Part a develops fundamental results; part b is a reading and research course: classic and current papers will be discussed, and students will do projects on current research topics. Instructor: Winfree.

Time & Place: 
BE 191a: Second term, 2011, Noyes 153, Tu 1-2:25pm, Th 1-2:25pm
BE 191b: Third Term, 2011, details TBA.

Syllabus (subject to change):

Note: reference links may require a Caltech IP address.

Homeworks

Grading Policy for BE 191a:
(Updated 2/17/2011) There will be homework sets roughly every other week (four total) and a final exam.
Homeworks: Homeworks will be graded on a {0,1,2} scale.

Note that getting a 2 does not necessarily mean it is 100% correct. An exemplary homework set will be chosen each week as a "solution set" and handed out in class (with the name hidden).
Final exam: The final will be a take-home problem sets and will consist of the same kind of questions as those constituting the homeworks, with no time limit. In other words they will not be difficult if you have been doing the homework and carefully reviewing the solution sets. The final will have ~5 questions on the material throughout the class. The exam will be graded more rigorously than the homework; clarity, correctness, and completeness will be essential.
Grade composition: Your class grade will be based on: 50% final, 50% homeworks.
Collaboration policy: For problem sets other than the final, you may discuss problems with other students, but what you turn in must be entirely written by you, including any program code. For the final, you may not discuss the problems with other students and all work must be entirely your own.

Grading Policy for BE 191b:
Your grade will be based on weekly reading and writing assignments, as well as a final project. The final project is due (TBA). Presentations will be scheduled (TBA).

Office hours: TBA

Resources: Reading Lists for BE 191b.

Expected background: (references coming)