Abstract

On distributed memory electronic computers, the implementation and association of fast parallel matrix multiplication algorithms has yielded astounding results and insights. In this discourse, we use the tools of molecular biology to demonstrate the theoretical encoding of Strassen’s fast matrix multiplication algorithm with DNA based on an n-moduli set in the residue number system, thereby demonstrating the viability of computational mathematics with DNA. As a result, a general scalable implementation of this model in the DNA computing paradigm is presented and can be generalized to the application of all fast matrix multiplication algorithms on a DNA computer. We also discuss the practical capabilities and issues of this scalable implementation. Fast methods of matrix computations with DNA are important because they also allow for the efficient implementation of other algorithms (that is inversion, computing determinants, and graph theory) with DNA.

Key words: DNA computing, residue number system, logic and arithmetic operations, Strassen algorithm.