Date: 01 Jun 2005

Self-organizing algorithms derived from RNA interactions

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We discuss algorithms based on the RNA interaction found in Nature. Molecular biology has reveiled that strands of RNA, besides being autocatalytic, can interact with each other. They play a double role of being information carriers and enzymes. The first role is realized by the 1-dimensional sequence of nucleotides on a strand of RNA, the second by the 3-dimensional form strands can assume under appropriate temperature and solvent conditions. We use this basic idea of having two alternative forms of the same sequence to propose a new Artificial Life algorithm. After a general introduction to the area we report our findings in a specific application studied recently: an algorithm which allows sequences of binary numbers to interact. We introduce folding methods to achieve 2-dimensional alternative forms of the sequences. Interactions between 1- and 2-dimensional forms of binary sequences generate new sequences, which compete with the original ones due to selection pressure. Starting from random sequences, replicating and self-replicating sequences are generated in considerable numbers. We follow the evolution of a number of sample simulations and analyse the resulting self-organising system.