CRN++: Molecular programming language

Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective represe...

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Vydáno v:Natural computing Ročník 19; číslo 2; s. 391 - 407
Hlavní autoři: Vasić, Marko, Soloveichik, David, Khurshid, Sarfraz
Médium: Journal Article
Jazyk:angličtina
Vydáno: Dordrecht Springer Netherlands 01.06.2020
Springer Nature B.V
Témata:
Algorithms
Artificial Intelligence
Biology
Chemical reactions
Complex Systems
Computation
Computer Science
Embedding
Error analysis
Evolutionary Biology
Microcontrollers
Nanofabrication
Processor Architectures
Programming languages
Reaction kinetics
Representations
Semantics
Theory of Computation
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ISSN:1567-7818, 1572-9796
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Shrnutí:Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representations that are faithful, efficient, and practical remains challenging . This paper introduces CRN ++, a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler translating CRN ++ programs into chemical reactions, thereby laying the foundation of a comprehensive framework for molecular programming. Our language addresses the key challenge of embedding familiar imperative constructs into a set of chemical reactions happening simultaneously and manipulating real-valued concentrations. Although some deviation from ideal output value cannot be avoided, we develop methods to minimize the error, and implement error analysis tools. We demonstrate the feasibility of using CRN ++on a suite of well-known algorithms for discrete and real-valued computation. CRN ++ can be easily extended to support new commands or chemical reaction implementations, and thus provides a foundation for developing more robust and practical molecular programs.
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ISSN:1567-7818
1572-9796
DOI:10.1007/s11047-019-09775-1