ALCH: An imperative language for chemical reaction network-controlled tile assembly

Abstract

Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals controlled by a chemical reaction network. This paper introduces ALCH, an imperative programming language for specifying CRN-TAM programs that can be compiled and simulated. ALCH includes standard language features such as Boolean variables, conditionals, loops, and CRN-TAM-specific constructs such as adding and removing tiles. ALCH also includes the branch and parallel structures which harness the nondeterministic and parallel nature of the CRN-TAM. ALCH also supports functional tileset specification. Using ALCH, we show that the discrete Sierpinski triangle and the discrete Sierpinski carpet can be strictly self-assembled in the CRN-TAM, which shows the CRN-TAM can self-assemble infinite shapes at scale 1 that the aTAM cannot. ALCH allows us to present these constructions at a high level, abstracting species and reactions into C-like code that is simpler to understand. We employ two new CRN-TAM techniques in our constructions. First, we use ALCH’s nondeterministic branching feature to probe previously placed tiles of the assembly and detect the presence and absence of tiles. Second, we use scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. This paper is an extension of our previous work, updated to include a Sierpinski carpet construction and the parallel command.