Programming in Biomolecular Computation
Electronic Notes in Theoretical Computer Science (ENTCS)
Computational biology: a programming perspective
Formal modeling
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Biological organisms are beautiful examples of programming. Theprogram and data are stored in biological molecules such as DNA,RNA, and proteins; the algorithms are carried out by molecular andbiochemical processes; and the end result is the creation andfunction of an organism. If we understood how to program molecularsystems, what could we create? Lifelike technologies whose basicoperations are chemical reactions? The fields of chemistry,physics, biology, and computer science are converging as we beginto synthesize molecules, molecular machines, and molecular systemsof ever increasing complexity, leading to subdisciplines such asDNA nanotechnology, DNA computing, and synthetic biology. Havingdemonstrated simple devices and systems -- self-assembledstructures, molecular motors, chemical logic gates -- researchersare now turning to the question of how to create large-scaleintegrated systems. To do so, we must learn how to managecomplexity: how to efficiently specify the structure and behaviorof intricate molecular systems, how to compile such specificationsdown to the design of molecules to be synthesized in the lab, andhow to ensure that such systems function robustly. These issueswill be illustrated for chemical logic circuits based on cascadesof DNA hybridization reactions.Bio Erik Winfree is an Associate Professor in Computer Science,Computation & Neural Systems, and Bioengineering at Caltech.Winfree is the recipient of the Feynman Prize for Nanotechnology(2006), the NSF PECASE/CAREER Award (2001), the ONR YoungInvestigators Award (2001), a MacArthur Fellowship (2000), and MITTechnology Review's first TR100 list of "top young innovators"(1999). Prior to joining the faculty at Caltech in 2000, Winfreewas a Lewis Thomas Postdoctoral Fellow in Molecular Biology atPrinceton, and a Visiting Scientist at the MIT AI Lab. Winfreereceived a B.S. in Mathematics w/ Computer Science from theUniversity of Chicago in 1991, and a Ph.D. in Computation &Neural Systems from Caltech in 1998. His website ishttp://dna.caltech.edu/~winfree/.