BE/CS/CNS/Bi 191ab:  Biomolecular Computation
Professor: Erik Winfree
Guest lecturers & TAs: Nadine Dabby, David Doty, Constantine Evans, Jongmin Kim, Lulu Qian, Joseph Schaeffer, Niranjan Srinivas, Damien Woods

This page is for Fall 2011. The previous incarnation is Winter/Spring 2011.
The next time BE/CS/CNS/Bi 191a will be taught is Winter 2013.
Description from the course catalog:
BE/CS/CNS/Bi 191 ab. Biomolecular Computation. 9 units (3-0-6) first 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. 191b is not offered in 2011-2012.

Time & Place: 
BE/CS 191a: First term, 2011, Annenberg 107, Tu & Th 10:30am-11:55am
BE/CS 191b: Will not be offered in the 2011-2012 academic year.

Office hours:
Wednesday October 12, 2-3pm, Moore 204 conference room.
Monday October 17, 2-3pm, Moore 204 conference room.
Monday October 24, 3-4pm, Moore 204 conference room.
Thursday October 27, 3-4pm, Moore 204 conference room.
Monday October 31, 3-4pm, Moore 204 conference room.
Tuesday November 8, 4-5pm, Moore 204 conference room.
Thursday November 10, 3-4pm, Moore 204 conference room.
Monday November 14, 4-5pm, Moore 204 conference room.
Thursday November 17, 3-4pm, Moore 204 conference room.
Tuesday November 22, 4-5pm, Moore 204 conference room.
Tuesday November 29, 4-5pm, Moore 204 conference room.
Monday Dec 5, 4-5pm, Moore 204 conference room.
Wednesday Dec 7, 4-5pm, Moore 204 conference room.

Syllabus (subject to change):

Note: reference links may require a Caltech IP address.

Homeworks

Grading Policy for BE 191a:
There will be roughly one problem per class lecture, with homework sets due roughly every other week. There is no midterm or final.
Homeworks: Homeworks will be graded on a 0-10 scale for each problem. For each homework set, an exemplary student solution will be chosen and handed out in class (with the name hidden).
Late policy: Late homework up to 24 hours late will be penalized by 10%, i.e. the score will be multiplied by 0.9 after grading. For two-day late HW (i.e up to 48 hours), the penalty will be 20%. The penalty increases by 10% per day, until a 9 day late homework's score is multiplied by 0.1, and a 10 day late homework gets no credit. The homework sets are hard, but ample time is given. Start as soon as they are handed out.
Grade composition: Your class grade will be based on homeworks only.
Collaboration policy: For all problem sets, you may discuss problems with other students prior to writing anything down, but what you turn in must be entirely written by you, by yourself, including any program code.

Helpful background: