TY - GEN
T1 - Synthesizing sequential register-based computation with biochemistry
AU - Shea, Adam
AU - Fett, Brian
AU - Riedel, Marc
AU - Parhi, Keshab K
PY - 2009/12/1
Y1 - 2009/12/1
N2 - 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.
AB - 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.
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M3 - Conference contribution
AN - SCOPUS:76349123592
SN - 9781605588001
T3 - IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD
SP - 136
EP - 143
BT - Proceedings of the 2009 IEEE/ACM International Conference on Computer-Aided Design - Digest of Technical Papers, ICCAD 2009
T2 - 2009 IEEE/ACM International Conference on Computer-Aided Design, ICCAD 2009
Y2 - 2 November 2009 through 5 November 2009
ER -