swMATH ID: 33637
Software Authors: Vasic, Marko; Soloveichik, David; Khurshid, Sarfraz
Description: 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 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 Open image in new window , a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler translating Open image in new window 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 Open image in new window on a suite of well-known algorithms for discrete and real-valued computation. Open image in new window 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.
Homepage: https://link.springer.com/chapter/10.1007%2F978-3-030-00030-1_1
Source Code: https://github.com/marko-vasic/crnPlusPlus
Related Software: Visual DSD; CRNSimulator
Cited in: 2 Publications

Cited in 1 Serial

1 Automatica

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