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Synthesizing sequential register-based computation with biochemistry

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4 Author(s)
Shea, A. ; Dept. of Electr. & Comput. Eng., Univ. of Minnesota, Twin Cities, Minneapolis, MN, USA ; Riedel, M. ; Fett, B. ; Parhi, K.

This paper presents a compilation strategy and a toolkit for biochemical reactions that perform sequential arithmetic computation on protein quantities, analogous to register-based computation in digital systems. From a Verilog-like input specification file, we generate biochemical reactions that produce output quantities as a function of input quantities, performing operations such as addition, subtraction, and multiplication. Sequential operations are implemented by transferring quantities between protein types, based on a clocking mechanism. Synthesis first is performed at a conceptual level, in terms of abstract biochemical reactions - a task analogous to technology-independent logic synthesis in circuit design. Then the results are mapped onto specific biochemical reactions, selected from libraries - a task analogous to technology mapping in circuit design. Our method targets the universal DNA substrate developed by Erik Win-free's group at Caltech as the experimental chassis. We demonstrate the algorithm on the synthesis of a variety of standard sequential functions: signal processing functions (FIR filters and IIR filters), vector multiplication, integration and differentiation. The designs are validated through transient stochastic simulation of the chemical kinetics.

Published in:

Computer-Aided Design - Digest of Technical Papers, 2009. ICCAD 2009. IEEE/ACM International Conference on

Date of Conference:

2-5 Nov. 2009