Synthesizing Configurable Biochemical Implementation of Linear Systems from Their Transfer Function Specifications.
The ability to engineer synthetic systems in the biochemical context is constantly being improved and has a profound societal impact. Linear system design is one of the most pervasive methods applied in control tasks, and its biochemical realization has been proposed by Oishi and Klavins and advanced further in recent years. However, several technical issues remain unsolved. Specifically, the design process is not fully automated from specification at the transfer function level, systems once designed often lack dynamic adaptivity to environmental changes, matching rate constants of reactions is not always possible, and implementation may be approximative and greatly deviate from the specifications. Building upon the work of Oishi and Klavins, this paper overcomes these issues by introducing a design flow that transforms a transfer-function specification of a linear system into a set of chemical reactions, whose input-output response precisely conforms to the specification. This system is implementable using the DNA strand displacement technique. The underlying configurability is embedded into primitive components and template modules, and thus the entire system is adaptive. Simulation of DNA strand displacement implementation confirmed the feasibility and superiority of the proposed synthesis flow.
Department of Physics, National Taiwan University, Taipei, Taiwan; Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan.
Tai-Yin
TY
Chiu
Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan; EPI Lifeware, Inria Paris-Rocquencourt, Rocquencourt, France.
Hui-Ju K
HJ
Chiang
Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan.
Ruei-Yang
RY
Huang
Graduate Institute of Electronics Engineering, National Taiwan University, Taipei, Taiwan; Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.
Jie-Hong R
JH
Jiang
EPI Lifeware, Inria Paris-Rocquencourt, Rocquencourt, France.
François
F
Fages
D002384:Catalysis; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D008962:Models, Theoretical; D058615:Synthetic Biology / Q000379:methods*
D004247:DNA