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Reactamole: functional reactive molecular programming

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Abstract

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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Notes

  1. Reactamole is available at https://github.com/digMP/haskell-reactamole.

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Acknowledgements

The authors also thank the anonymous reviewers for their suggestions and feedback.

Funding

This work was funded in part by National Science Foundation Grants 2049911, 1651817, 1545028, 1900716, and 1909688.

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Author notes

  1. Titus H. Klinge, James I. Lathrop, Peter-Michael Osera and Allison Rogers have contributed equally to this work.

Authors and Affiliations

  1. Computer Science Department, Iowa State University, Ames, 50011, IA, USA

    Titus H. Klinge & James I. Lathrop

  2. Computer Science Department, Grinnell College, Grinnell, 50112, IA, USA

    Peter-Michael Osera & Allison Rogers

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  1. Titus H. Klinge
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  2. James I. Lathrop
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  3. Peter-Michael Osera
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  4. Allison Rogers
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Correspondence to James I. Lathrop.

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Klinge, T.H., Lathrop, J.I., Osera, PM. et al. Reactamole: functional reactive molecular programming. Nat Comput (2024). https://doi.org/10.1007/s11047-024-09982-5

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