Synthesizing sequential register-based computation with biochemistry

Adam Shea, Brian Fett, Marc Riedel, Keshab K Parhi

Research output: Chapter in Book/Report/Conference proceedingConference contribution


This paper presents a compilation strategy and a toolkit for biochemical reactions that perform sequential arithmetic computation on protein quantities, analogous to registerbased 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 Winfree'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.

Original languageEnglish (US)
Title of host publicationProceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009
Number of pages8
StatePublished - Dec 1 2009
Event2009 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2009 - San Jose, CA, United States
Duration: Nov 2 2009Nov 5 2009

Publication series

NameIEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD
ISSN (Print)1092-3152


Other2009 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2009
Country/TerritoryUnited States
CitySan Jose, CA


Dive into the research topics of 'Synthesizing sequential register-based computation with biochemistry'. Together they form a unique fingerprint.

Cite this