NDLI: Synthesizing sequential register-based computation with biochemistry

Content Provider	IEEE Xplore Digital Library
Author	Shea, A. Riedel, M. Fett, B. Parhi, K.
Copyright Year	2009
Description	Author affiliation: Department of Electrical and Computer Engineering, University of Minnesota, Twin Cities, Minneapolis, Minnesota 55455 (Shea, A.; Riedel, M.; Fett, B.; Parhi, K.)
Abstract	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.
Starting Page	136
Ending Page	143
File Size	371721
Page Count	8
File Format	PDF
ISBN	9781605588001
ISSN	10923152
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2009-11-02
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Association for Computing Machinery, Inc. (ACM)
Subject Keyword	Biochemistry Circuit synthesis Proteins Signal processing algorithms Digital arithmetic Digital systems Hardware design languages Clocks Logic design Logic circuits
Content Type	Text
Resource Type	Article
Subject	Computer Graphics and Computer-Aided Design Computer Science Applications Software

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