1 Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU2 FLinT - Center for Fundamental Living Technology, Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU3 European Centre for Living Technology, S.Marco 2940, Venice4 SDU eScience Centre, Department of Mathematics and Computer Science (IMADA), Faculty of Science, SDU5 ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich6 The Lancet Lab, Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot7 SDU eScience Centre, Department of Mathematics and Computer Science (IMADA), Faculty of Science, SDU8 Department of Physics, Chemistry and Pharmacy, Faculty of Science, SDU
Exploiting Compartmentalization for the Synthesis of Branched Polymers
In this paper, we propose the MATCHIT Automaton (MA), a theoretical framework that shows how to improve the yield of the synthesis of chemical polymer reactions. This is achieved by separating sub-steps of the path of syn- thesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of compartments. We describe the MA in mathematical terms and show how it can be configured automatically in order to synthesize a branched target polymer given as input. We discuss how the MA models compartmentalized structures found in cells, such as the endoplasmatic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers. Lastly, we show exam- ples of artificial branched polymers and discuss how the MA can be configured to synthesize them with maximal yield.
Computational and Mathematical Methods in Medicine (print Edition), 2013