BE/CS/CNS/Bi 191ab: Biomolecular Computation
Professor: Erik Winfree
Winter term: Guest lecturer, class #1: David Doty. Teaching assistant: Constantine Evans
This page is for Winter/Spring 2013. The previous incarnation was Fall 2011.
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: none. Recommended: ChE/BE 163, 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/CS 191a: Winter 2013, Annenberg 107, Tu & Th 10:30am-11:55am
BE/CS 191b: Spring 2013, Annenberg 106, Th 7:30-9:55pm
TA: Friday January 11th from 3-4pm in the Moore 204 conference room, and
every Friday thereafter at the same time.
Please start your homework set early, and come to the first relevant TA session.
The homework will usually be too much to do at the last minute, and planning for this is your responsibility.
Prof: Thursdays from 3-4pm in Moore 204. This is for issues that can't be handled by the TA only.
None. Please attend class. Everything you need to know should be presented there. The references suggested below are optional further reading, but neither sufficient nor necessary.
The syllabus as presented gives you a rough idea of what will be in
the class, but it is subject to change in detail. The topics and
references should be considered final only on the day of the lecture,
Note: reference links may require a Caltech IP address.
- Introduction and overview -- 1 lecture
- Jan 8: computation in the cell and the promise of molecular programming.
- Chemical reaction networks (CRNs) -- 5 lectures (tools: GEC)
- Jan 10: continuous mass action model, kinetics, steady-state, equilibrium -- illustrated via chemotaxis circuitry.
[optional refs on mass action, a bacterial chemotaxis example]
- Jan 15: mass action dynamical systems for amplifiers, switches, and memories. [optional ref with sample CRNs.]
- Jan 17: mass action dynamical systems for oscillators, chaos, and everything. [optional ref on Korzuhin's Theorem.]
- Jan 22: digital circuits using mass action, signal loss and restoration, digital abstraction, logic gates.
[optional refs on digital circuits and an alternative design]
- Jan 24: discrete stochastic model, kinetics and probabilities; computing with counts.
[optional refs on stochastic,
more computing, and
even more computing.]
- Biochemistry & combinatorial CRNs -- 3 lectures
- Nucleic acid circuits -- 4 lectures (tools: DSD and NUPACK)
- Passive self-assembly -- 4 lectures (tools: xgrow and ISU TAS)
- Feb 21: introduction to experimental and theoretical systems for tile-based self-assembly.
[lecture slides in .ppt]
[optional refs on experiments on
DNA computing & linear self-assembly,
Sierpinski in DNA, and
copying and counting from a seed]
- Feb 26: algorithmic patterns & and growing squares -- aTAM programming
[optional refs on squares, and
- Feb 28: computation & growing algorithmic shapes -- aTAM programming
[optional refs on arbitrary shapes]
- Mar 5: errors and error-correction -- self-healing, kinetics, thermodynamics, proofreading, nucleation -- kTAM simulations
[optional refs on
- Amorphous computing and synthetic biology -- 2 lectures (tools: gro)
homework will be handed out in class every other Tuesday, and due by
email as a single PDF file before 11:59pm on Monday 13 days
thereafter. There will be five homework sets.
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.
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.
Accompanying Files for Homework:
For problem set 3, stack_machine.dna.
- 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