Erik Winfree

Computer Science
Computation and Neural Systems
Caltech, MS 136-93, Moore 204B
Pasadena, CA 91125 [USA]
Voice: (626) 395-6246
FAX: (626) 584-0630
Assistant: Lucinda Acosta, x5707

My group has been a part of The Molecular Programming Project

In March 2016, I organized a symposium celebrating Ten Years of DNA Origami

Research Interests Group research on biomolecular computation
    - DNA computation, DNA nanotechnology, and Molecular Programming
    - Algorithmic self-assembly using passive tiles
    - Algorithmic development using molecular robots
    - Cell-free biochemical circuits and systems
    - Enzyme-free DNA strand displacement circuits
    - Self-replicating molecular systems, evolution, and the origin of life
    - Multistranded DNA and RNA interaction thermodynamics, kinetics, and biophysics
    - Programming languages and compilers for nucleic acid systems
    - Fault-tolerance, self-healing, and randomness in molecular systems
DNA Group Research Publications. My publications on Google Scholar and on on Web of Science.
DNA Lab Wiki.
Teaching Office hours: Moore 204, 1:30-2:00pm Tuesdays, Winter Term 2018.

CNS/Bi/Ph/CS 187: Neural Computation (Fall 2000- 2006, 2007, 2008) [used to be CNS/Bi/Ph 185: Collective Computation].
CNS/CS/Bi 288: DNA and Molecular Computation (Winter 2001)
BE 168: Reading the Bioengineering Literature (Winter 2013, 2015, 2017)
BE 201: Reading the Bioengineering Literature (Winter 2018, 2019)
BE/CS/CNS/Bi 191ab: Biomolecular Computation (Winter/Spring 2002, 2005, 2007, 2010, 2011, Fall 2011, Winter/Spring 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2021)
CS/EE/Ma 129ab and/or c: Information and Complexity (Fall 2002, 2003, Winter/Spring 2007, 2008, Fall/Winter/Spring 2009-2010, Fall 2011)

The 2011 Caltech BIOMOD Team.
Computing Beyond Silicon Summer School (June 17 - July 17, 2002; June 14 - July 9, 2004) [news stories]
Collaborators, Past, Present (and Future?) Len Adleman's group (USC, Computer Science).
David Anderson (University of Wisconsin, Madison, Mathematics).
Marc Bockrath's group (University of California, Riverside, Physics).
Shuki Bruck's group (Caltech, Electrical Engineering).
Luca Cardelli (Oxford, Computer Science).
Ho-Lin Chen (National Taiwan University, Electrical Engineering).
Anne Condon (U. British Columbia, Computer Science).
Matt Cook's group (ETH, Neuroinformatics).
David Doty (UC Davis, Computer Science).
Jonathan Doye's group (Oxford, Theoretical Chemistry).
Andy Ellington's group (UT Austin, Molecular Biosciences).
Deborah Fygenson's group (UCSB, Physics).
Peter Gacs (Boston University, Computer Science).
Bill Goddard's group (Caltech, Chemistry).
Ashish Goel's group (Stanford, MSE).
Manoj Gopalkrishnan (IIT Bombay, Electrical Engineering).
Eric Klavins's group (U. Washington-Seattle, Electrical Engineering).
Ard Louis's group (Oxford, Theoretical Physics).
Hideo Mabuchi's group (Stanford, Applied Physics).
Satoshi Murata's group (Tohoko University, Mechanical Engineering).
Richard Murray's group (Caltech, Control and Dynamical Systems).
Arvind Murugan's group (University of Chicago, Physics).
Tom Ouldridge's group (Imperial College London, Bioengineering).
Niles Pierce's group (Caltech, Bioengineering).
Lulu Qian's group (Caltech, Bioengineering).
John Reif's group (Duke University, Computer Science).
Paul Rothemund (Caltech, Bioengineering).
Grzegorz Rozenberg (Leiden University, Computer Science).
Rebecca Schulman's group (Johns Hopkins, Chemical and Biomolecular Engineering).
Georg Seelig (U. Washington-Seattle, Computer Science and Engineering).
Ned Seeman's group (New York University, Chemistry).
Fritz Simmel's group (Tech. U. Munich, Physics).
David Soloveichik's group (UY Austing, Electrical and Computer Engineering).
Milan Stojanovic (Columbia University, Systems Biology).
Andrew Turberfield's group (Oxford, Condensed Matter Physics).
Nils Walter's group (University of Michigan, Chemistry).
Damien Woods' group (Maynooth University, Hamilton Institute).
Hao Yan's group (Arizona State University, Chemistry and Biochemistry).
Peng Yin's group (Harvard, Wyss Institute).
Bernard Yurke (Boise State University, Materials Science and Engineering).
Dave Zhang's group (Rice, Bioengineering).
Awards and Recognition My C.V. (long form)
MIT's Technology Review Magazine's TR100 award (1999).
MIT's Technology Review Magazine has two issues where they describe my work: November/December 1999 (TR100 Award) and May/June 2000.
Tulip Award in DNA Computing (2000).
MacArthur Fellowship (2000).
NSF PECASE award (2001) and ONR YIP award (2001).
Foresight Nanotech Institute's Feynman Prize in Theory and Experiment, shared with Paul Rothemund (2006).
I was interviewed by Discover Magazine in the July-August 2009 issue.
I was also interviewed by Genetic Engineering & Biotechnology News in October, 2009.
Elected as a Fellow of the American Association for the Advancement of Science (AAAS) in 2015. Spotlight interview
Workshops and Conferences Co-organizer: Ten Years of DNA Origami, March 14-16, 2016.
Co-organizer: Verification of Engineered Molecular Devices and Programs (VEMDP), July 19, 2015.
Co-organizer: Advances in Molecular Programming and Computing: Toward Chemistry as a New Information Technology, May 2-4, 2013. (Workshop report in English, Japanese.)
Co-organizer: 17th International Conference on DNA Computing and Molecular Programming, September 19 - 23, 2011.
Co-organizer: CBCD workshop on Self-Replicating Chemical Systems, August 27 - 28, 2007.
Co-organizer: Banff workshop on Stochasticity in Biochemical Reaction Networks, June 15 - 17, 2007.
Co-organizer: CBCD workshop on Engineering a DNA World, Jan 6 - 8, 2005.
Co-organizer: Banff workshop on Dynamics, Control and Computation in Biochemical Networks August 21 - 26, 2004.
Co-organizer: 5th DNA-Based Computers Meeting, MIT, June 14-15, 1999.
Co-organizer: DIMACS Workshop on Evolution as Computation, Princeton, January 11 - 12, 1999.
Professional Societies ISNSCE ("Essence"): International Society for Nanoscale Science, Computation, and Engineering, which sponsors two annual conferences: FNANO and DNA Computing and Molecular Programming.
ACM: Association for Computing Machinery.
ACS: American Chemical Society.
MAA: Mathematical Association of America.
AMS: American Mathematical Society.
AAAS: American Association for the Advancement of Science.
Past Life I was a Visiting Scientist in Tom Knight's group in 2000 (when he was in the MIT AI Lab).
I was a Postdoctoral Scholar in Stan Leibler's group group in 1998-1999 (when he was at Princeton University).
I was a graduate student in John Hopfield's group from 1994-1998 (when he was at Caltech) and in Al Barr's group from 1992-1994 at Caltech.
As a graduate student, I also spent time in John Abelson's lab (at Caltech) and in Ned Seeman's lab (at NYU), and I collaborated with Len Adleman (at USC).
Hence: ---(old defunct molecular computation pages)--- and: ---(old SIRDS page)---
From 1991-1992, I worked with Stephen Wolfram and Matthew Cook.
I was an undergraduate at the University of Chicago from 1987-1991, during which time I spent half a year doing math in Budapest.
I went to Evanston Township High School and the best math summer camp ever.
First science teacher: Dad. His 1964 essay on "The Scientist as Poet".
A nice essay about going to grad school that quotes my dad at the end.
Artistic Activities Sometime I shall see the world, my first poem, age 8, although I was trying to write a rock song. Now with DALL-E illustrations.
Collaboration with an exceptional artist: Ann Erpino.
A Carpet of Algorithms, a whimsical play about a visit to a scientific museum, with illustrations related to our paper.
She Dreams of Molecules, a poem for my wife on the occasion of her tenure, with DALL-E illustrations. (Chinese)
The Rain in Seattle, a poem for my mother and step-father on the occasion of their 40th anniversary, with DALL-E illustrations.
Coming of Age Ceremony of the Dream Siblings, a poem with DALL-E illustrations. (HTML)
State of mind, Memory, Nico's song, Hold on change, Don't no one know why, and Faultline, my brother's songs with my DALL-E powered videos.
Family The love of my life, Lulu Qian. My sister, Rachael Winfree. My brother, Chris Woollcott. My mother, Trish Woollcott. My step-father, Phil Woollcott. My father, Art Winfree.

My uncle's experience as artist-in-residence for the National Parks in Alaska. (He and his wife have an art studio.)

Information about my food allergies