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Programmability of Chemical Reaction Networks
"... Summary. 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 wellstirred solution according to standard c ..."
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Summary. 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 wellstirred 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
Arithmetic and the Incompleteness Theorems
, 2000
"... this paper please consult me first, via my home page. ..."
Global semantic typing for inductive and coinductive computing
"... Common datatypes, such as N, can be identified with term algebras. Thus each type can be construed as a global set; e.g. for N this global set is instantiated in each structure S to the denotations in S of the unary numerals. We can then consider each declarative program as an axiomatic theory, and ..."
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Common datatypes, such as N, can be identified with term algebras. Thus each type can be construed as a global set; e.g. for N this global set is instantiated in each structure S to the denotations in S of the unary numerals. We can then consider each declarative program as an axiomatic theory, and assigns to it a semantic (Currystyle) type in each structure. This leads to the intrinsic theories of [18], which provide a purely logical framework for reasoning about programs and their types. The framework is of interest because of its close fit with syntactic, semantic, and proof theoretic fundamentals of formal logic. This paper extends the framework to data given by coinductive as well as inductive declarations. We prove a Canonicity Theorem, stating that the denotational semantics of an equational program P, understood operationally, has type τ over the canonical model iff P, understood as a formula has type τ in every “datacorrect ” structure. In addition we show that every intrinsic theory is interpretable in a conservative extension of firstorder arithmetic. 1998 ACM Subject Classification F.3 Logics and meanings of programs