Chemical reaction networks (CRNs) are an important tool for molecular programming. This field is
rapidly expanding our ability to deploy computer programs into biological systems for various applications.
However, CRNs are also difficult to work with due to their massively parallel nature, leading
to the need for higher-level languages that allow for more straightforward computation with CRNs.
Recently, research has been conducted into various higher-level languages for deterministic CRNs but
modeling CRN parallelism, managing error accumulation, and finding natural CRN representations
are ongoing challenges. We introduce Reactamole, a higher-level language for deterministic CRNs
that utilizes the functional reactive programming (FRP) paradigm to represent CRNs as a reactive
dataflow network. Reactamole equates a CRN with a functional reactive program, implementing the
key primitives of the FRP paradigm directly as CRNs. The functional nature of Reactamole makes
reasoning about molecular programs easier, and its strong static typing allows us to ensure that a CRN
is well-formed by virtue of being well-typed. In this paper, we describe the design of Reactamole and
how we use CRNs to represent the common datatypes and operations found in FRP. We demonstrate
the potential of this functional reactive approach to molecular programming by giving an extended
example where a CRN is constructed using FRP to modulate and demodulate an amplitude-modulated
signal. We also show how Reactamole can be used to specify abstract CRNs whose structure depends
on the reactions and species of its input, allowing users to specify more general CRN behaviors.
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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 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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- Award ID(s):
- 1652824
- PAR ID:
- 10109801
- Date Published:
- Journal Name:
- DNA Computing and Molecular Programming. DNA 2018.
- Volume:
- 11145
- Page Range / eLocation ID:
- 1-18
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1007/978-3-030-00030-1_1
