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
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.
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.
- Introduction and overview -- 1 lecture
- Sep 27: computation in the cell and the promise of molecular programming.
- Chemical reaction networks (CRNs) -- 4 lectures (tools: GEC)
- Biochemistry & combinatorial CRNs -- 2 lectures
- Nucleic acid circuits -- 5 lectures (tools: DSD and NUPACK)
- Passive self-assembly -- 3 lectures (tools: xgrow and ISU TAS)
- Active self-assembly and molecular robotics -- 3 lectures
- Amorphous computing and synthetic biology -- 1 lecture (tools: gro)
- Homework set #1 was handed out October 4th and is due by email October 17th (Monday) before 11:59pm.
- Homework set #2 was handed out October 18th and is due by email October 31th (Monday) before 11:59pm.
- Homework set #3 was handed out November 1st and is due by email November 14th (Monday) before 11:59pm.
[HW had wrong due date, so Nov 15 will also be accepted.]
- Homework set #4 was handed out November 15th and is due by email December 1st (Thursday) before 11:59pm. Happy Thanksgiving!
- Homework set #5 was handed out December 1st and is due by email December 9th (Friday) before 11:59pm.
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
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.
- Python, Matlab, or Mathematica programming
- Digital AND OR NOT circuits
- Finite State Machines and Regular Languages
- Turing machines & Register machines
- Cellular automata
- Chemical reaction networks; mass-action and stochastic kinetics and thermodynamics
- Basic molecular biology, central dogma enzymes, cytoskeleton
- DNA secondary structure, folding kinetics and thermodynamics,
hybridization & dissociation rates, toeholds, 3-way & 4-way