A Tissue P System and a DNA Microfluidic Device for Solving the Shortest Common Superstring Problem

Abstract

This paper describes a tissue P system for solving the Shortest Common Superstring Problem in linear time. This tissue P system is well suited for parallel and distributed implementation using a micro°uidic device working with DNA strands. The tP system is not based on the usual brute force generate/test technique applied in DNA computing, but builds the space solution gradually. The possible solutions/superstrings are build step by step through the parallel distributed combination of strings using the overlapping concatenation operation. Moreover, the DNA micro°uidic device solves the problem autonomously, without the need of external control or manipulation.