An extended cellular space method for simulating autocatalytic oligonucleotides

Self-replicating nucleotides and other self-replicating molecules are an active area of study today by organic chemists. Such studies are important for improving our understanding of the origins of life. Computational studies of self-replicating molecules could increase our insight into their properties, but existing computational techniques have been limited in their usefulness for such reactions (numerical simulation of differential equations requires reaction rate constants that are difficult to obtain, cellular automata models are too restrictive for modeling molecular movements and bindings, etc.). We have thus developed an efficient modified cellular automata method that supports the study of self-replicating oligonucleotides. We explain this method and illustrate its use with a specific self-replicating (autocatalytic) deoxyribohexanucleotide.