Design of Cellular Automata Rules for Biomolecules

Abstract

The second chapter concentrates on establishing Cellular Automata (CA) representation of biomolecules. Current life form has evolved around three biomolecules DNA, RNA and Protein. DNA/RNA strands display a sugar–phosphate backbone to which nucleotide bases are bonded. Simple CA rules have been designed to represent the information content of the molecular structure of nucleic acid and the base triplets are referred to as codons. Proteins are the workhorse of living cells. Its building blocks are amino acids. A codon gets translated to an amino acid molecule. All the amino acids have a common backbone, which is interconnected to form a protein chain. In this background, simple CA rules designed for codons are employed for modelling amino acid backbone. Further, the side chain of an amino acid is also digitally coded with an 8-bit string used as the initial input for CA cells designed for backbone. Design of CA rules for micromolecules of life is referred to as bottom-up first principle informatics modelling. The evolution of CA designed with such rules generates certain model parameters. These parameters are mapped to the features extracted out of wet lab experimental results on these biomolecules. The top-down validation of the CA model is undertaken in the subsequent three chapters.

“I believe that new mathematical schemata, new systems of axioms, certainly new systems of mathematical structures will be suggested by the study of the living world”.

—Stanislaw Ulam