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. 1. Introduction Recently, small scale personal manufacturing has seen a rapid increase in popularity with emerging technologies such as 3D printing. In place of central production and physical distribution of goods, personal manufacturing offers a transfer of information (e.g., designs, protocols) followed by in-place, customizable production. Although mainly discussed in the context of macroscale personal manufacturing (i.e., 3D printing), personal manufacturing is also found in the domain of (bio-)chemistry. In custom oligonucleotide and peptide synthesis, the information, that is, DNA or protein sequence, is sent by the customer to the supplier. Even though the synthesized DNA oligonucleotides or peptides are shipped back to the customer (i.e., transfer of goods), this example demonstrates how transferred information can lead to in-place, customizable production of (bio)chemical goods. However, often the desired product cannot be synthesized via either one-pot synthesis or sequential one-pot synthesis. Consequently, distinct confinement and transport of substances and an elaborate temporal and spatial reaction management are needed. The European Commission funded project MATCHIT (Matrix for Chemical IT [1, 2]) aims to open the domain of chemistry for distributed manufacturing by implementing unconventional embedded computation systems. By employing addressable soft colloid supermolecular chemical containers (chemtainers) that act both as transport and reaction vessels and that are interfaced with electronic computers via microelectromechanical systems (MEMS), the topological
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