Programming Biological Cells

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.

My 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, I 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, I combined matching gates to implement several small circuits. To aid in this biocircuit design process I implemented BioSpice, a prototype genetic circuit simulation and verification tool.

Finally, I 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.

My contributions so far:

"Cellular Computation and Communications using Engineered Genetic Regulatory Networks", Faculty Candidate Job Talk, March/April 2001:
Talk (PowerPoint file)

"Engineered Communications for Microbial Robotics", DNA6 Sixth International Meeting on DNA Based Computers, June 2000:
Paper available in the following formats:
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Talk (PowerPoint file, html, )

"Digitally Programmed Cells", Workshop on Biomolecular Computation: Its Potential and Applications, October 1999:
Talk available in the following formats:
, PowerPoint

"Toward in-vivo digital circuits", Dimacs Workshop on Evolution as Computation, January 1999:
Paper available in the following formats:
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Talk (PowerPoint file, html)

PhD Proposal, MIT Electrical Engineering and Computer Science Department, January, 1999:
Available in the following formats:
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"Programming Biological Cells", ASPLOS-VIII, Eighth International Conference on Architectural Support for Programming Languages and Operating Systems, Wild and Crazy Ideas Session, October 1998:
Abstract available in the following formats:
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Talk (PowerPoint file, html)


Other relevant links:

My microbial engineering links


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Page Last Modified -- 04/18/2001