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Title: The MATCHIT automaton : exploiting compartmentalization for the synthesis of branched polymers
Authors : Weyland, Mathias S.
Fellermann, Harold
Hadorn, Maik
Sorek, Daniel
Lancet, Doron
Rasmussen, Steen
Füchslin, Rudolf Marcel
Published in : Computational and Mathematical Methods in Medicine
Volume(Issue) : 2013
Issue : 467428
Publisher / Ed. Institution : Hindawi
Issue Date: 2013
License (according to publishing contract) : CC BY 3.0: Namensnennung 3.0 Unported
Type of review: Peer review (Publication)
Language : English
Subject (DDC) : 005: Computer programming, programs and data
540: Chemistry
Abstract: We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield.
Departement: School of Engineering
Organisational Unit: Institute of Applied Mathematics and Physics (IAMP)
Publication type: Article in scientific Journal
DOI : 10.1155/2013/467428
ISSN: 1748-670X
Appears in Collections:Publikationen School of Engineering

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