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Computational and Mathematical Methods in Medicine
Volume 2013 (2013), Article ID 467428, 8 pages
http://dx.doi.org/10.1155/2013/467428
Research Article

The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers

1European Centre for Living Technology, S. Marco 2940, 30124 Venice, Italy
2Center for Fundamental Living Technology (FLinT), Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark
3Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
4The Lancet Lab, Department of Molecular Genetics, Weizmann Institute of Science, 76100 Rehovot, Israel
5Santa Fe Institute, Santa Fe, NM 87501, USA
6Institute of Applied Mathematics and Physics, School of Engineering, Zurich University of Applied Sciences, 8401 Winterthur, Switzerland

Received 31 October 2013; Accepted 8 December 2013

Academic Editor: Roberto Serra

Copyright © 2013 Mathias S. Weyland et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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.