Parallel molecular computation
Proceedings of the seventh annual ACM symposium on Parallel algorithms and architectures
Artificial chemistries—a review
Artificial Life
Evolvable self-replicating molecules in an artificial chemistry
Artificial Life
Explicit collision simulation of chemical reactions in a graph based artificial chemistry
ECAL'05 Proceedings of the 8th European conference on Advances in Artificial Life
Modeling biochemical pathways using an artificial chemistry
Artificial Life
Robustness to Code and Data Deletion in Autocatalytic Quines
Transactions on Computational Systems Biology X
An artificial-chemistry approach to generating polyphonic musical phrases
Evo'08 Proceedings of the 2008 conference on Applications of evolutionary computing
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Artificial chemistries are mainly used to construct virtual systems that are expected to show behavior similar to living systems. In this study, we explore possibilities of applying an artificial chemistry to modeling natural biochemical systems---or, to be specific, molecular computing systems---and show that it may be a useful modeling tool for molecular computation. We previously proposed an artificial chemistry based on string pattern matching and recombination. This article first demonstrates that this artificial chemistry is computationally universal if it has only rules that have one reactant or two reactants. We think this is a good property of an artificial chemistry that models molecular computing, because natural elementary chemical reactions, on which molecular computing is based, are mostly unimolecular or bimolecular. Then we give two illustrative example models for DNA computing in our artificial chemistry: one is for the type of computation called the Adleman-Lipton paradigm, and the other is for a DNA implementation of a finite automaton. Through the construction of these models we observe preferred properties of the artificial chemistry for modeling molecular computing, such as having no spatial structure and being flexible in choosing levels of abstraction.