The biomolecular computation paradigm: A survey in massive biological computation

Abstract

Biomolecular computation is the scientific field focusing on the theory and practice of encoding combinatorial problems in ordi-nary DNA strands and applying standard biology lab operations such as cleansing and complementary sequence generation to them in order to compute an exact solution. The primary advantage offered by this computational paradigm is massive parallelism as the solution space is simultaneously searched. On the other hand, factors that need to addressed under this model are the DNA volume growth and computational errors attributed to inexact DNA matching. Biomolecular computation additionally paves the way for two-and three-dimensional self assemblying biological tiles which are closely linked at a theoretical level to a Turing machine, establishing thus its computational power. Applications include medium sized instances of TSP and the evaluation of the output of bounded fan-out Boolean circuits.