Biological organisms sense their environment, process information, and
continuously react to both internal and external stimuli. We can now
harness organisms as computational substrates, and extend their
behavior by embedding biochemical logic circuitry that controls intra-
and inter-cellular processes. The engineering and construction of
reliable in-vivo logic circuitry enables a wide range of
programmed applications. The application areas include drug and
biomaterial manufacturing, programmed therapeutics, embedded
intelligence in materials, sensor/effector arrays, gene therapy, and
nanoscale fabrication.
Our research uses computer engineering principles of abstraction,
composition, and interface specifications to build programmable
bio-organisms with sensors and actuators precisely controlled by logic
circuitry. Here, recombinant DNA-binding proteins represent signals,
and recombinant genes perform the computation by regulating protein
expression. To demonstrate basic cellular computation and
intercellular communication, we have constructed and tested
biochemical gates in Escherichia coli that implement the
AND, NOT and IMPLIES logic operations.
After measuring and modifying the ``device physics'' of these gates, we
combined matching gates to implement several small circuits. To aid
in this biocircuit design process we implemented BioSpice, a prototype
genetic circuit simulation and verification tool.
Finally, we defined the Microbial Colony Language (MCL), a simple
programming paradigm that could be instantiated in-vivo with
small circuits and intercellular communications. This
intermediate-level programming language is used to explore how to
achieve globally coordinated behavior (e.g. pattern formation) from a
large number of unreliable computing elements such as programmed cells
that are constrained to communicate locally.
Contributions so far:
 | AI Movie, Press demo material, April
2001:
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| "Cellular Computation and Communications using
Engineered Genetic Regulatory Networks", Ron Weiss, Faculty Candidate
Job Talk, March/April 2001:
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| "Engineered Communications for Microbial Robotics",
Ron Weiss and Tom Knight, DNA6 Sixth
International Meeting on DNA Based Computers, June
2000:
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| "Digitally Programmed Cells", Ron Weiss, Workshop on
Biomolecular Computation: Its Potential and Applications, October
1999:
 | Talk available in the following formats:
 , PowerPoint
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| "Toward in-vivo digital circuits", Ron Weiss and Geo
Homsy and Tom Knight, Dimacs Workshop
on Evolution as Computation, January 1999:
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| PhD Proposal, Ron Weiss, MIT Electrical Engineering and Computer Science Department, January, 1999:
| Available in the following formats:
 ,  ,
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| "Programming Biological Cells", Ron Weiss and Geo
Homsy and Rahdika Nagpal, ASPLOS-VIII, Eighth
International Conference on Architectural Support for Programming
Languages and Operating Systems, Wild
and Crazy Ideas Session, October 1998:
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