Research Interests

Molecular programming: the rational design of molecular interactions for synthetic biology, nanotechnology, and bioengineering. Engineering networks of nucleic-acid interactions from scratch.
The theoretical foundation of chemical computation. Can principles of theoretical computer science and distributed computing help us understand complex molecular interactions?
The knowledge representation scheme of the primate brain, and its basic computational primitives.

Recent Presentations

An introduction to strand displacement cascades for the Foresight Institute Conference (Palo Alto, Jan 2013): An Artificial "Biochemistry" with DNA
Paper presented at DNA Computing and Molecular Programming 18 (Aarhus, Denmark, Aug 2012): Deterministic Function Computation with Chemical Reaction Networks
My tutorial talk for DNA Computing and Molecular Programming 17 (Pasadena, Aug 2011): The Programming Language of Chemical Kinetics, and How To Discipline Your DNA Molecules using Strand Displacement Cascades
High-level introduction to algorithmic self-assembly and stochastic chemical reaction networks as computer-theoretic models: Computer-Theoretic Abstractions for Molecular Programming
On algorithmic behavior in chemical reaction networks and implementing arbitrary chemical reaction networks with DNA: Programming Well-Mixed Chemical Kinetics
On provable asymptotic bounds on the number of leaps for tau-leaping as a function of maximum molecular count: Bounded Tau-leaping and Robust Chemical Reaction Networks

Publications [Google scholar profile]

Erik Winfree's publications page includes his "whimsical" descriptions for most of these papers. [α]=alphabetical author order following the common mathematics and theoretical computer science convention.

[α] Ho-Lin Chen, David Doty, David Soloveichik, "Deterministic Function Computation with Chemical Reaction Networks".
[ Preliminary version in DNA Computing and Molecular Programming 18, 2012: .pdf ]
Lulu Qian, David Soloveichik, Erik Winfree, "Efficient Turing-universal computation with DNA polymers".
[ Journal version in preparation. ]
[ Extended abstract in Proceedings of DNA Computing 16, 2010: .pdf ]
David Soloveichik, Georg Seelig, Erik Winfree, "DNA as a Universal Substrate for Chemical Kinetics".
[ PNAS 107 (12): 5393-5398, 2010: .pdf paper and .pdf supplementary information ]
[ Preliminary extended abstract in Proceedings of DNA Computing 14, LNCS 5347:57-69, 2009: .pdf ]
Georg Seelig, David Soloveichik, "Time-Complexity of Multilayered DNA Strand Displacement Circuits".
[ Revised version (improved lemmas 1 and 4): .pdf ]
[ Preliminary extended abstract in Proceedings of DNA Computing 15, LNCS 5877: 144-153, 2009: .pdf ]
David Soloveichik, "Statistical Learning of Arbitrary Computable Classifiers".
[ Preprint: .pdf ]
Matt Cook, David Soloveichik, Erik Winfree, Shuki Bruck, "Programmability of Chemical Reaction Networks".
[ Algorithmic Bioprocesses, (Eds. Condon, Harel, Kok, Salomaa, Winfree), Springer, pp. 543-584, 2009 ]
[ Preprint: .pdf ]
David Soloveichik, "Robust Stochastic Chemical Reaction Networks and Bounded Tau-Leaping".
[ Journal of Computational Biology 16(3): 501-522, 2009 ]
[ arXiv preprint: cs.CC/0803.1030 ]
David Soloveichik, Matt Cook, Erik Winfree, Shuki Bruck, "Computation with Finite Stochastic Chemical Reaction Networks".
[ Natural Computing, (on line Feb 2008), or Technical Report: CaltechPARADISE:2007.ETR085: .pdf ]
David Soloveichik, Matthew Cook, Erik Winfree, "Combining Self-Healing and Proofreading in Self-Assembly".
[ Natural Computing, (on line July 2007): .pdf ]
Georg Seelig, David Soloveichik, David Yu Zhang, Erik Winfree, "Enzyme-Free Nucleic Acid Logic Circuits".
[ Science 314:1585-1588, 2006: .pdf paper and .pdf supplementary information ]
[ Also see Walter Fontana's Perspectives essay, Udi Shapiro's News and Views essay ]
[ Our related patent is #20070072215: "Nucleic acid-based logic circuits" ]
David Soloveichik and Erik Winfree, "Complexity of Compact Proofreading for Self-Assembled Patterns".
[ Proceeding of DNA Computing 11, LNCS 3892: 305-324, 2006: .pdf ]
David Soloveichik and Erik Winfree, "The Computational Power of Benenson Automata".
[ Theoretical Computer Science 244(2-3):279-297, 2005: .pdf paper and .pdf erratum ]
David Soloveichik and Erik Winfree, "Complexity of Self-Assembled Shapes".
[ SIAM Journal on Computing 36 (6): 1544-1569, 2007: .pdf ]
[ Extended abstract in Proceedings of DNA Computing 10, LNCS 3384:344-354, 2005: .pdf ]

Link Support/Hobbies

Mathematica package I wrote for inputting chemical reaction networks and simulating them: CRNSimulator.m
My iPhone app is available in the App Store: Buzzbuka. I support jailbreaking.
I build and fly RC airplanes. Hobby-Lobby has movies of many RC aircraft in action.