CNS/CS/Bi 288:  DNA and Molecular Computation
Professor: Erik Winfree

Time & Place:  Second term, 2001, Beckman Institute 23, Tuesdays, 5:30-7:00pm.  Pizza provided.

Plan:  We will read roughly 40 papers on the physics of computation, biochemical and cellular computation,
DNA nanotechnology and DNA computing.    Students will present the papers in class, and will write a final paper.

Objectives: To identify key concepts and results in the readings, understand and illustrate them using simple examples, critique the limitations of the results, and brainstorm.  Students should not attempt to present all aspects of the all papers, but rather should choose one or two key issues and explore them in detail during the presentation.   The presenter should assume that everyone in the class has read the required readings (but maybe doesn't fully understand it yet).

Grading will be based on (1) participation in class discussions, including 3 short discussion questions (less than 1 page, typed) handed in before each class, (2) presentation of an article, (3) a 5-page final paper investigating a topic discussed in the class.

Office hours: Moore 204, Tuesdays, 2:30-3:30pm
Pre-presentation discussion (one week ahead): Moore 204, Tuesdays, 2:00-2:30pm

Topics:

Jan 9:  Physics of computation: energy and reversibility [Ben Rahn and Joseph Schaeffer]

Jan 16: Cellular computing:  chemotaxis, biochemical networks [Chris Hart and Ewa Matejska]

Jan 23:  Genetic regulatory networks: models and synthetic design [Ryan Mackey and Roger Revilla]

Jan 30:  Synthetic biochemical systems: predator-prey, simulations, noise, and robustness [Jongmin Kim and Paul Rothemund]

Feb 6:  In vitro evolution of DNA and RNA [Leila Reddy and Rory Sayres]

Feb 13: DNA computing for combinatorial search [Geoffrey Hom and Matt Cook]

Feb 20: Thermodynamics and kinetics of DNA hybridization and folding [Ben Rahn and Caglar Tanrikulu]

Feb 27: Molecular engineering and DNA nanotechnology: DNA structures, beacons, tweezers, and catalysts [Ryan Mackey and Leila Reddy]

Mar 6: Computation by molecular self-assembly and molecular folding [Geoffrey Hom and Matt Cook]

Mar 16: No class... final paper due.

Papers:

Jan 9: Physics of Computation

Jan 16: Cellular computing
  • D. Bray, "Protein Molecules as Computational Elements in Living Cells." Nature. 376: 307-312 (1995).
  • D. C. Hauri and J. Ross, "A Model of Excitation and Adaptation in Bacterial Chemotaxis." Biophysical Journal 68: 708-722 (1995).
  • M. O. Magnasco, "Chemical Kinetics is Turing Universal." Phys. Rev. Let. 78: 1190-1193 (1997).
  • A. Hjelmfelt, E. D. Weinberger, and J. Ross, "Chemical Implementation of Neural Networks and Turing Machines." Proc. Natl. Acad. Sci. USA88: 10983-10987 (1991).
  • (optional) A. Hjelmfelt and J. Ross, "Chemical Implementation and Thermodynamics of Collective Neural Networks." Proc. Natl. Acad. Sci. USA 89: 388-391 (1992).
  • Jan 23:  Genetic regulatory networks Jan 30:  Synthetic biochemical systems


    Feb 6:  In vitro evolution of DNA and RNA

    Feb 13: DNA computing for combinatorial search Feb 20: Thermodynamics and kinetics of DNA hybridization and folding Feb 27: Molecular engineering and DNA nanotechnology Mar 6: Computation by molecular self-assembly and molecular folding Grand Total:  38 required, 14 optional