Specification of the stringmol chemical programming language version 0.1

Research output: Working paper


This report describes in detail version 0.1 of a specification for a nonstandard computational model that emulates the reactivity of enzymes in bacterial cells. The model is an artificial chemistry in which the unique properties of each molecular species is encoded as a sequence of symbols. The model has a very simple cell-level representation consisting of a mixing volume and mixing equation. There is no distinction between genotype and phenotype, or data and program. Randomly selected molecules are subject to a stochastic binding test, in which their identifying sequences are subjected to a complementary alignment process. If the bind is successful, the molecules are combined to form a computational entity to run the reaction between them. At this point the sequence acts as a microprogram. These microprograms can perform a range of tasks, much as a chemical reaction can. Our first chemistry within this model solves the problem of designing a chemical "replicase", capable of creating copies of itself such that it can replenish a population of molecules that are subject to a decay process. This report gives detail to the model, describes the replicase molecule and its function, and shows an "invasion when rare" experiment.
Original languageUndefined/Unknown
Publication statusPublished - 2010

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