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Programmability of Chemical Reaction Networks

Cook, Matthew and Soloveichik, David and Winfree, Erik and Bruck, Jehoshua (2009) Programmability of Chemical Reaction Networks. In: Algorithmic Bioprocesses. Natural Computing Series. Springer-Verlag , Berlin, pp. 543-584. ISBN 978-3-540-88868-0.

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Motivated by the intriguing complexity of biochemical circuitry within individual cells we study Stochastic Chemical Reaction Networks (SCRNs), a formal model that considers a set of chemical reactions acting on a finite number of molecules in a well-stirred solution according to standard chemical kinetics equations. SCRNs have been widely used for describing naturally occurring (bio)chemical systems, and with the advent of synthetic biology they become a promising language for the design of artificial biochemical circuits. Our interest here is the computational power of SCRNs and how they relate to more conventional models of computation. We survey known connections and give new connections between SCRNs and Boolean Logic Circuits, Vector Addition Systems, Petri nets, Gate Implementability, Primitive Recursive Functions, Register Machines, Fractran, and Turing Machines. A theme to these investigations is the thin line between decidable and undecidable questions about SCRN behavior.

Item Type:Book Section
Related URLs:
URLURL TypeDescription DOIArticle ItemTechnical Report
Soloveichik, David0000-0002-2585-4120
Winfree, Erik0000-0002-5899-7523
Bruck, Jehoshua0000-0001-8474-0812
Additional Information:© 2009 Springer-Verlag Berlin Heidelberg. The research was supported in part by the “Alpha Project” at the Center for Genomic Experimentation and Computation, an NIH Center of Excellence (grant number P50 HG02370), as well as NSF Grants No. 0523761 and 0728703 to EW and NIMH Training Grant MH19138-15.
Funding AgencyGrant Number
NIHP50 HG02370
NIH Predoctoral FellowshipMH19138-15
Series Name:Natural Computing Series
Record Number:CaltechAUTHORS:20111020-103016495
Persistent URL:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27327
Deposited By: Tony Diaz
Deposited On:24 Oct 2011 22:18
Last Modified:21 Feb 2020 22:19

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