Programmability of Chemical Reaction Networks

Cook, Matthew and Soloveichik, David and Winfree, Erik and Bruck, Jehoshua (2008) Programmability of Chemical Reaction Networks. Technical Report. California Institute of Technology, Pasadena, CA. [CaltechPARADISE:2008.ETR090]

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Abstract

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.

EPrint Type:	Monograph (Technical Report)
Additional Information:	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. Also available http://www.paradise.caltech.edu/papers/etr090.pdf
Subjects:	All Records
ID Code:	119
Deposited By:	Caltech Library System
Deposited On:	23 September 2008
Record Number:	CaltechPARADISE:2008.ETR090
Official Persistent URL:	http://resolver.caltech.edu/CaltechPARADISE:2008.ETR090
Official Citation:	Matthew Cook, David Soloveichik, Erik Winfree, and Jehoshua Bruck (2008) Programmability of Chemical Reaction Networks. Technical Report. California Institute of Technology, Pasadena, CA. [CaltechPARADISE:2008.ETR090]
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