A chemical compiler for the synthesis of branched oligomers on standardized chemical reaction structures

Weyland, Mathias S.; Flumini, Dandolo; Schneider, Johannes J.; Faggian, Alessia; Patiño Diaz, Aitor; Füchslin, Rudolf Marcel

doi:10.1162/isal_a_00648

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-28699

Publication type:	Conference paper
Type of review:	Peer review (publication)
Title:	A chemical compiler for the synthesis of branched oligomers on standardized chemical reaction structures
Authors:	Weyland, Mathias S. Flumini, Dandolo Schneider, Johannes J. Faggian, Alessia Patiño Diaz, Aitor Füchslin, Rudolf Marcel
et. al:	No
DOI:	10.1162/isal_a_00648 10.21256/zhaw-28699
Proceedings:	ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference
Page(s):	105
Conference details:	International Conference on Artificial Life (ALIFE), Sapporo, Japan, 24-28 July 2023
Issue Date:	24-Jul-2023
Publisher / Ed. Institution:	MIT Press
Publisher / Ed. Institution:	Cambridge
Language:	English
Subjects:	Chemical compiler; Branched oligomer; Chemical reaction
Subject (DDC):	540: Chemistry
Abstract:	This research paper presents a chemical compiler developed to find optimal configurations of a platform for synthesizing specific branched oligomers in an artificial chemistry, along with exemplary compiler output and benchmarks where the platform configuration suggested by the compiler is compared to other configurations in simulation. The compiler operates as a pipeline with two stages: labelling and optimization. The report explains the structure of the compiler target and its interpretation, followed by a code walk-through of the compiler stages with code snippets and examples. The compiler can be used as a code generator for reactions in a chemical simulator and to derive loading schemes for multilevel droplets. The results obtained in simulations suggest that the container system can efficiently optimize the yield of coupled reaction networks and that multi-level droplets can lead to significant improvements.
URI:	https://digitalcollection.zhaw.ch/handle/11475/28699
Fulltext version:	Published version
License (according to publishing contract):	CC BY 4.0: Attribution 4.0 International
Departement:	School of Engineering
Organisational Unit:	Institute of Applied Mathematics and Physics (IAMP)
Published as part of the ZHAW project:	ACDC – Artificial Cells with Distributed Cores to Decipher Protein Function
Appears in collections:	Publikationen School of Engineering

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Weyland, M. S., Flumini, D., Schneider, J. J., Faggian, A., Patiño Diaz, A., & Füchslin, R. M. (2023). A chemical compiler for the synthesis of branched oligomers on standardized chemical reaction structures [Conference paper]. ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference, 105. https://doi.org/10.1162/isal_a_00648

Weyland, M.S. et al. (2023) ‘A chemical compiler for the synthesis of branched oligomers on standardized chemical reaction structures’, in ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference. Cambridge: MIT Press, p. 105. Available at: https://doi.org/10.1162/isal_a_00648.

M. S. Weyland, D. Flumini, J. J. Schneider, A. Faggian, A. Patiño Diaz, and R. M. Füchslin, “A chemical compiler for the synthesis of branched oligomers on standardized chemical reaction structures,” in ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference, Jul. 2023, p. 105. doi: 10.1162/isal_a_00648.

WEYLAND, Mathias S., Dandolo FLUMINI, Johannes J. SCHNEIDER, Alessia FAGGIAN, Aitor PATIÑO DIAZ und Rudolf Marcel FÜCHSLIN, 2023. A chemical compiler for the synthesis of branched oligomers on standardized chemical reaction structures. In: ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference. Conference paper. Cambridge: MIT Press. 24 Juli 2023. S. 105

Weyland, Mathias S., Dandolo Flumini, Johannes J. Schneider, Alessia Faggian, Aitor Patiño Diaz, and Rudolf Marcel Füchslin. 2023. “A Chemical Compiler for the Synthesis of Branched Oligomers on Standardized Chemical Reaction Structures.” Conference paper. In ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference, 105. Cambridge: MIT Press. https://doi.org/10.1162/isal_a_00648.

Weyland, Mathias S., et al. “A Chemical Compiler for the Synthesis of Branched Oligomers on Standardized Chemical Reaction Structures.” ALIFE 2023: Ghost in the Machine : Proceedings of the 2023 Artificial Life Conference, MIT Press, 2023, p. 105, https://doi.org/10.1162/isal_a_00648.