A magic pot: self-assembly computation revisited

Authors:
Takashi Yokomori;Yasubumi Sakakibara;Satoshi Kobayashi
Affiliations:
Department of Mathematics, School of Education, Waseda University, 1-6-1 Nishi-waseda, Shinjuku-ku, Tokyo 169-8050, Japan;Department of Information Sciences, Tokyo Denki University, Hiki-gun, Saitama 350-0394, Japan;Department of Computer Science and Information Mathematics, University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo 182, Japan
Venue:
Formal and natural computing
Year:
2002

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Abstract

Molecular computing is a novel computing paradigm recently emerged from groundbreaking wet lab experiments by Adleman in 1994. His experimental work marks a potential capability and feasibility of "one pot" computing with molecules for solving hard problems of practical size.This paper concerns a molecular computing paradigm based on "self-assembly" and "screening mechanism". After a brief getting back to and reviewing Adleman's original work, we propose a new molecular implementation method based on length-only encoding, which leads us to much simpler molecular implementation techniques to solve graph problems.With two examples, we demonstrate the effectiveness of the molecular implementation method for one pot computing based on self-assembly: one is Nondeterministic Finite Automaton Pot and the other Hamiltonian Path Problem Pot.